diff --git a/.gitignore b/.gitignore index 1832fed..78f7552 100644 --- a/.gitignore +++ b/.gitignore @@ -38,3 +38,5 @@ recount.all.data.plier.RData # Ignore hidden metadata files ._* + +Rplots\.pdf diff --git a/NARES/NARES_PC_scatter_with_batch_correct.pdf b/NARES/NARES_PC_scatter_with_batch_correct.pdf index bbaf223..4882a44 100644 Binary files a/NARES/NARES_PC_scatter_with_batch_correct.pdf and b/NARES/NARES_PC_scatter_with_batch_correct.pdf differ diff --git a/NARES/processed/NARES_SCANfast_ComBat.pcl b/NARES/processed/NARES_SCANfast_ComBat.pcl index 62cf524..21e777b 100644 --- a/NARES/processed/NARES_SCANfast_ComBat.pcl +++ b/NARES/processed/NARES_SCANfast_ComBat.pcl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:9751a84f5aae82081723287eab80bbb88b3853b962651b6d725d8c8e7c1a160f -size 28716222 +oid sha256:b4030615ba9a6f5070be3adc3c0a2e640791689f357e2f1000a3f39dd66fdc42 +size 28714201 diff --git a/NARES/processed/NARES_hugene10st_SCANfast.pcl b/NARES/processed/NARES_hugene10st_SCANfast.pcl index ea58381..09dfb8c 100644 --- a/NARES/processed/NARES_hugene10st_SCANfast.pcl +++ b/NARES/processed/NARES_hugene10st_SCANfast.pcl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:88a8be05784696023cc26d9eb369420960f0118644276d1a26e1e861260a8bf2 -size 27551801 +oid sha256:e2b531b1f7c333ac7ca2ec426fb34543574e744edbf1a13cf3b489eede1a57e3 +size 27542721 diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 0000000..3139d15 --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,36 @@ +FROM rocker/tidyverse:3.4.3 + +RUN apt-get update && apt-get install -y \ + git \ + wget \ + curl + +RUN R install2.r --error \ + --deps TRUE \ + foreach \ + parallel \ + RCurl + +# bioconductor packages +RUN R -e "BiocInstaller::biocLite(c('pd.hg.u133.plus.2', 'pd.hg.u133a', 'pd.hg.u133b', 'pd.hg.u95av2', 'pd.hugene.1.0.st.v1', 'pd.hugene.1.1.st.v1', 'SCAN.UPC', 'affy', 'affyio', 'preprocessCore', 'affxparser', 'illuminaHumanv4.db', 'hgug4112a.db', 'biomaRt', 'org.Hs.eg.db', 'qvalue'))" + +# brainarray for affymetrix arrays (v22.0.0) +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133plus2hsentrezgprobe_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133ahsentrezgprobe_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133bhsentrezgprobe_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu95av2hsentrezgprobe_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hugene11sthsentrezgprobe_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hugene10sthsentrezgprobe_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133plus2hsentrezgcdf_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133ahsentrezgcdf_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133bhsentrezgcdf_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hgu95av2hsentrezgcdf_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hugene11sthsentrezgcdf_22.0.0.tar.gz')" +RUN R -e "devtools::install_url('http://mbni.org/customcdf/22.0.0/entrezg.download/hugene10sthsentrezgcdf_22.0.0.tar.gz')" + + +# packages from github +RUN R -e "devtools::install_github('wgmao/PLIER', ref = 'a2d4a2aa343f9ed4b9b945c04326bebd31533d4d', dependencies = TRUE)" +RUN R -e "devtools::install_github('greenelab/TDM', ref = '0bb5b7e4f2478295c9889aa1bf3cf91f1db11006', dependencies = TRUE)" + +RUN R -e "install.packages('doParallel')" diff --git a/docker/list_user_installed_R_packages.R b/docker/list_user_installed_R_packages.R new file mode 100644 index 0000000..a975470 --- /dev/null +++ b/docker/list_user_installed_R_packages.R @@ -0,0 +1,12 @@ +# J. Taroni 2018 +# Get list of installed R packages on Docker image +# Adapted from: +# https://www.r-bloggers.com/list-of-user-installed-r-packages-and-their-versions/ +# https://stackoverflow.com/questions/38481980/get-the-list-of-installed-packages-by-user-in-r + +packages.df <- as.data.frame(installed.packages()[, c(1, 3:4)]) +packages.df <- packages.df[is.na(packages.df$Priority), 1:2, drop=FALSE] + +sink(file.path("docker", "user_installed_R_packages.txt")) +print(packages.df, row.names=FALSE) +sink() diff --git a/docker/user_installed_R_packages.txt b/docker/user_installed_R_packages.txt new file mode 100644 index 0000000..c6d299b --- /dev/null +++ b/docker/user_installed_R_packages.txt @@ -0,0 +1,214 @@ + Package Version + acepack 1.4.1 + affxparser 1.50.0 + affy 1.56.0 + affyio 1.48.0 + annotate 1.56.1 + AnnotationDbi 1.40.0 + assertthat 0.2.0 + backports 1.1.2 + base64enc 0.1-3 + BH 1.66.0-1 + bindr 0.1 + bindrcpp 0.2 + Biobase 2.38.0 + BiocGenerics 0.24.0 + BiocInstaller 1.28.0 + BiocParallel 1.12.0 + biomaRt 2.34.2 + Biostrings 2.46.0 + bit 1.1-12 + bit64 0.9-7 + bitops 1.0-6 + blob 1.1.0 + brew 1.0-6 + broom 0.4.3 + callr 2.0.2 + caTools 1.17.1 + cellranger 1.1.0 + checkmate 1.8.5 + cli 1.0.0 + colorspace 1.3-2 + commonmark 1.4 + covr 3.0.1 + crayon 1.3.4 + curl 3.1 + data.table 1.10.4-3 + DBI 0.7 + dbplyr 1.2.1 + debugme 1.1.0 + DelayedArray 0.4.1 + desc 1.1.1 + devtools 1.13.5 + dichromat 2.0-0 + digest 0.6.15 + docopt 0.4.5 + doParallel 1.0.11 + dplyr 0.7.4 + dtplyr 0.0.2 + evaluate 0.10.1 + feather 0.3.1 + ff 2.2-13 + forcats 0.3.0 + foreach 1.4.4 + formatR 1.5 + Formula 1.2-2 + futile.logger 1.4.3 + futile.options 1.0.0 + gdata 2.18.0 + gdtools 0.1.7 + genefilter 1.60.0 + GenomeInfoDb 1.14.0 + GenomeInfoDbData 1.0.0 + GenomicRanges 1.30.3 + GEOquery 2.46.15 + ggplot2 2.2.1 + ggplot2movies 0.0.1 + git2r 0.21.0 + glmnet 2.0-13 + glue 1.2.0 + gmailr 0.7.1 + gplots 3.0.1 + gridExtra 2.3 + gtable 0.2.0 + gtools 3.5.0 + haven 1.1.1 + hexbin 1.27.2 + hgu133ahsentrezgcdf 22.0.0 + hgu133ahsentrezgprobe 22.0.0 + hgu133bhsentrezgcdf 22.0.0 + hgu133bhsentrezgprobe 22.0.0 + hgu133plus2hsentrezgcdf 22.0.0 + hgu133plus2hsentrezgprobe 22.0.0 + hgu95av2hsentrezgcdf 22.0.0 + hgu95av2hsentrezgprobe 22.0.0 + hgug4112a.db 3.2.3 + highr 0.6 + Hmisc 4.1-1 + hms 0.4.1 + htmlTable 1.11.2 + htmltools 0.3.6 + htmlwidgets 1.0 + httpuv 1.3.6 + httr 1.3.1 + hugene10sthsentrezgcdf 22.0.0 + hugene10sthsentrezgprobe 22.0.0 + hugene11sthsentrezgcdf 22.0.0 + hugene11sthsentrezgprobe 22.0.0 + hunspell 2.9 + igraph 1.1.2 + illuminaHumanv4.db 1.26.0 + IRanges 2.12.0 + irlba 2.3.2 + iterators 1.0.9 + jsonlite 1.5 + knitr 1.20 + labeling 0.3 + Lahman 6.0-0 + lambda.r 1.2 + latticeExtra 0.6-28 + lazyeval 0.2.1 + limma 3.34.9 + lintr 1.0.2 + littler 0.3.3 + lubridate 1.7.3 + magrittr 1.5 + mapproj 1.2-5 + maps 3.2.0 + maptools 0.9-2 + markdown 0.8 + MatrixModels 0.4-1 + matrixStats 0.53.1 + memoise 1.1.0 + microbenchmark 1.4-4 + mime 0.5 + mnormt 1.5-5 + mockery 0.4.1 + modelr 0.1.1 + multcomp 1.4-8 + munsell 0.4.3 + mvtnorm 1.0-7 + nycflights13 0.2.2 + oligo 1.42.0 + oligoClasses 1.40.0 + openssl 1.0 + org.Hs.eg.db 3.5.0 + pd.hg.u133.plus.2 3.12.0 + pd.hg.u133a 3.12.0 + pd.hg.u133b 3.12.0 + pd.hg.u95av2 3.12.0 + pd.hugene.1.0.st.v1 3.14.1 + pd.hugene.1.1.st.v1 3.14.1 + pheatmap 1.0.8 + pillar 1.2.1 + pingr 1.1.2 + pkgconfig 2.0.1 + PLIER 0.99.0 + plogr 0.1-1 + plyr 1.8.4 + praise 1.0.0 + preprocessCore 1.40.0 + prettyunits 1.0.2 + progress 1.1.2 + psych 1.7.8 + purrr 0.2.4 + quantreg 5.35 + qvalue 2.10.0 + R6 2.2.2 + RColorBrewer 1.1-2 + Rcpp 0.12.15 + RCurl 1.95-4.10 + readr 1.1.1 + readxl 1.0.0 + rematch 1.0.1 + remotes 1.1.1 + reprex 0.1.2 + reshape2 1.4.3 + rex 1.1.2 + rlang 0.2.0 + rmarkdown 1.8 + RMySQL 0.10.14 + roxygen2 6.0.1 + RPostgreSQL 0.6-2 + rprojroot 1.3-2 + RSQLite 2.0 + rstudioapi 0.7 + rsvd 0.9 + rversions 1.0.3 + rvest 0.3.2 + S4Vectors 0.16.0 + sandwich 2.4-0 + scales 0.5.0 + SCAN.UPC 2.20.0 + selectr 0.3-1 + shiny 1.0.5 + snow 0.4-2 + sourcetools 0.1.6 + sp 1.2-7 + SparseM 1.77 + stringdist 0.9.4.6 + stringi 1.1.6 + stringr 1.3.0 + SummarizedExperiment 1.8.1 + sva 3.26.0 + svglite 1.2.1 + TDM 0.3 + testit 0.7 + testthat 2.0.0 + TH.data 1.0-8 + tibble 1.4.2 + tidyr 0.8.0 + tidyselect 0.2.4 + tidyverse 1.2.1 + utf8 1.1.3 + viridis 0.5.0 + viridisLite 0.3.0 + whisker 0.3-2 + withr 2.1.1 + XML 3.98-1.10 + xml2 1.2.0 + xtable 1.8-2 + XVector 0.18.0 + yaml 2.1.17 + zlibbioc 1.24.0 + zoo 1.8-1 diff --git a/isolated-cell-pop/E-MTAB-2452_PCA_scatter_cell_type.pdf b/isolated-cell-pop/E-MTAB-2452_PCA_scatter_cell_type.pdf index 728c628..f6b5edd 100644 Binary files a/isolated-cell-pop/E-MTAB-2452_PCA_scatter_cell_type.pdf and b/isolated-cell-pop/E-MTAB-2452_PCA_scatter_cell_type.pdf differ diff --git a/isolated-cell-pop/processed/E-MTAB-2452_hugene11st_SCANfast.pcl b/isolated-cell-pop/processed/E-MTAB-2452_hugene11st_SCANfast.pcl index b0093a0..d949f89 100644 --- a/isolated-cell-pop/processed/E-MTAB-2452_hugene11st_SCANfast.pcl +++ b/isolated-cell-pop/processed/E-MTAB-2452_hugene11st_SCANfast.pcl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a249d1ddf12ffe47cb49c18d181383307d810fb11ed65ab2e299a223d42feec6 -size 16364008 +oid sha256:1a33d6dc3796409196fb88ec4ea8bfa551442fda087758ce72df0cf09d9f765e +size 16358121 diff --git a/sle-wb/02-calculate_spearman_affy_norm.R b/sle-wb/02-calculate_spearman_affy_norm.R index df573bf..149ba89 100644 --- a/sle-wb/02-calculate_spearman_affy_norm.R +++ b/sle-wb/02-calculate_spearman_affy_norm.R @@ -87,6 +87,8 @@ CompareSamplesPlotWrapper <- function(processed.dir, png.lead, function(f) sub(".*\\_", "", sub("_([^_]*)$", "", f)))) + platforms <- platforms[grepl("hgu", platforms)] + # for each platform for (plt in platforms) { diff --git a/sle-wb/diagrams/SLE-WB_selected_normalization_flowchart.png b/sle-wb/diagrams/SLE-WB_selected_normalization_flowchart.png index 8cea697..77a8d6c 100644 Binary files a/sle-wb/diagrams/SLE-WB_selected_normalization_flowchart.png and b/sle-wb/diagrams/SLE-WB_selected_normalization_flowchart.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.png b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.png index 052c20b..5ab33fc 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.png and b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.tsv b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.tsv index 40eccc3..81dea90 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_no.transform.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.719613257054696 -PC2 0.778752014167953 -PC3 0.818469460904513 -PC4 0.840750812307368 -PC5 0.859417961468562 +PC1 0.719195490028333 +PC2 0.778441415090079 +PC3 0.818254325770668 +PC4 0.840513867481337 +PC5 0.859185095462936 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.png b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.png index 9e1fed2..68b823f 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.png and b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.tsv b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.tsv index fbf10bc..26cdeba 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.after.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.643553803255725 -PC2 0.75185071203084 -PC3 0.797812363918736 -PC4 0.820004655365133 -PC5 0.8382113999406 +PC1 0.64331957608224 +PC2 0.751744198021767 +PC3 0.797718070379041 +PC4 0.81987379920512 +PC5 0.838091806794775 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.png b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.png index 6ab5dde..a4c5f06 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.png and b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.tsv b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.tsv index 7a5dcf1..734bd61 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_RMA_PC1-5_pairs_zto.before.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.238368049353571 -PC2 0.370181339219669 -PC3 0.435996104307166 -PC4 0.486643920868974 -PC5 0.516392902732684 +PC1 0.237965511035396 +PC2 0.3699417171876 +PC3 0.435803905195611 +PC4 0.486459091188161 +PC5 0.516211496672587 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.png b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.png index a0c8dbf..8ca2d96 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.png and b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.tsv b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.tsv index 1e707ad..f048ca2 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_no.transform.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.566067468113633 -PC2 0.659907596480561 -PC3 0.715506748965104 -PC4 0.756431911267807 -PC5 0.785072638756046 +PC1 0.56636882225646 +PC2 0.660153018484501 +PC3 0.715676021912042 +PC4 0.756585982088227 +PC5 0.785198449823178 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.png b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.png index 674a944..a991a7f 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.png and b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.tsv b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.tsv index d62de9e..1b5b52d 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.after.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.535603866969345 -PC2 0.651031074010261 -PC3 0.688416375086289 -PC4 0.721565328849104 -PC5 0.738576444935881 +PC1 0.535968177687654 +PC2 0.651198024224915 +PC3 0.688573002223942 +PC4 0.721706513584657 +PC5 0.738724111447259 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.png b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.png index 4b9206e..4a62fc2 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.png and b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.tsv b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.tsv index 7887638..1b228f4 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_SCAN_PC1-5_pairs_zto.before.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.221525601492806 -PC2 0.401550674445085 -PC3 0.461953932860628 -PC4 0.513577212610772 -PC5 0.540286690702352 +PC1 0.221498959514109 +PC2 0.401466795588395 +PC3 0.461965892500508 +PC4 0.51359517447216 +PC5 0.540318478249624 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.png b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.png index 4ac17d3..d5f0587 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.png and b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.tsv b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.tsv index e0162ef..151e9b5 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_no.transform.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.563109512056118 -PC2 0.656474974893193 -PC3 0.712575808570986 -PC4 0.753517289646143 -PC5 0.782092109886793 +PC1 0.563497771389573 +PC2 0.656798461140344 +PC3 0.712814404758625 +PC4 0.753738041186644 +PC5 0.782282742965279 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.png b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.png index 53f2cf4..1f3b535 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.png and b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.tsv b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.tsv index 9e8867f..a96ca27 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.after.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.534516911086129 -PC2 0.647483735366384 -PC3 0.684202498446857 -PC4 0.717176853931279 -PC5 0.734709417928961 +PC1 0.534857479663515 +PC2 0.647655030805677 +PC3 0.684360488879948 +PC4 0.717332073871017 +PC5 0.734873202789474 diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.png b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.png index 3fa961e..dd0f819 100644 Binary files a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.png and b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.png differ diff --git a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.tsv b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.tsv index b5c5db2..9a8728a 100644 --- a/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.tsv +++ b/sle-wb/plots/PCA/HGU133PLUS2_SCANfast_PC1-5_pairs_zto.before.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.218668288534673 -PC2 0.381516913978744 -PC3 0.446312471700543 -PC4 0.49862910452827 -PC5 0.526129591486157 +PC1 0.218726363691638 +PC2 0.381571003382186 +PC3 0.446446009335291 +PC4 0.498754044261779 +PC5 0.526278795431108 diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.png b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.png index d09df17..85da5e4 100644 Binary files a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.png and b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.png differ diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.tsv b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.tsv index 7d0e005..f31577b 100644 --- a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.tsv +++ b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_no.transform.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.414714065333539 -PC2 0.574202823363504 -PC3 0.661649921386675 -PC4 0.729941089418135 -PC5 0.7687751656184 +PC1 0.414466488794187 +PC2 0.57389453569493 +PC3 0.661469511348125 +PC4 0.729904689319816 +PC5 0.768757852366813 diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.png b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.png index 70a3aad..4c9bd90 100644 Binary files a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.png and b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.png differ diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.tsv b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.tsv index 409ef31..668daf7 100644 --- a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.tsv +++ b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.after.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.356119356432109 -PC2 0.493345308018337 -PC3 0.586422070551057 -PC4 0.649919356791546 -PC5 0.693060416884434 +PC1 0.356229259592836 +PC2 0.493353569248797 +PC3 0.586545002248656 +PC4 0.65007740569024 +PC5 0.69321628254821 diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.png b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.png index 6f52e4d..e39999d 100644 Binary files a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.png and b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.png differ diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.tsv b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.tsv index 8bc1bab..db98562 100644 --- a/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.tsv +++ b/sle-wb/plots/PCA/SLE_WB_all_microarray_QN_PC1-5_zto.before.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.279016191508999 -PC2 0.374962969165165 -PC3 0.439168567211033 -PC4 0.479149533762764 -PC5 0.502220141029585 +PC1 0.27895778917934 +PC2 0.374894351575738 +PC3 0.439115251526305 +PC4 0.479085706788835 +PC5 0.502166854445793 diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.png b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.png index aa14ef1..fc00fa7 100644 Binary files a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.png and b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.png differ diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.tsv b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.tsv index 5a73a5a..481b7e3 100644 --- a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.tsv +++ b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_no.transform.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.863457420165437 -PC2 0.93265572326637 -PC3 0.960465907040871 -PC4 0.969350416061673 -PC5 0.973776614346316 +PC1 0.863421693552575 +PC2 0.93262433003629 +PC3 0.960446724962493 +PC4 0.969332085157842 +PC5 0.973761990868359 diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.png b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.png index 99b39e0..9bdab5a 100644 Binary files a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.png and b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.png differ diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.tsv b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.tsv index 6008844..952a297 100644 --- a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.tsv +++ b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.after.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.853377715817386 -PC2 0.931245545548363 -PC3 0.963217433698452 -PC4 0.971870926061195 -PC5 0.975240407976156 +PC1 0.853318861287836 +PC2 0.93122429220467 +PC3 0.963200805680526 +PC4 0.971857023490957 +PC5 0.975229423471802 diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.png b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.png index 8298072..495af10 100644 Binary files a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.png and b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.png differ diff --git a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.tsv b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.tsv index 1d1d1c5..c028aa0 100644 --- a/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.tsv +++ b/sle-wb/plots/PCA/SLE_WB_all_microarray_without_QN_PC1-5_zto.before.tsv @@ -1,6 +1,6 @@ Principal Component cumulative variance explained -PC1 0.44629634761757 -PC2 0.544863765262412 -PC3 0.593986188490653 -PC4 0.620096524164796 -PC5 0.638200810741853 +PC1 0.446305977755825 +PC2 0.54488026746902 +PC3 0.594032207804947 +PC4 0.62014300735656 +PC5 0.638256232057372 diff --git a/sle-wb/plots/PCA/viz_all_microarray_colorkey.png b/sle-wb/plots/PCA/viz_all_microarray_colorkey.png index 73f20b9..a5c682d 100644 Binary files a/sle-wb/plots/PCA/viz_all_microarray_colorkey.png and b/sle-wb/plots/PCA/viz_all_microarray_colorkey.png differ diff --git a/sle-wb/plots/norm_method_correlation/SLE-WB_affy_norm_correlation_hgu133a_RMA_v_SCAN.png 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