Error in (function (classes, fdef, mtable)

[CWYuan08]

您好，请问以下的报错如何解决？

cm <- clusterData(exps ,

•               cluster.method = "mfuzz",
  

•               cluster.num = 12)
  

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘exprs’ for signature ‘"ExpressionSet"’

非常感谢！！

[junjunlab]

重新安装试试

[CWYuan08]

不好意思已重新安装过了，但还是有这个error

[junjunlab]

没有安装好吧？

[CWYuan08]

您好，我试着重新安装了几次， 但是用cluster.method=“mfuzz“ 就会有同样的报错 （Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘exprs’ for signature ‘"ExpressionSet）， 如果用”kmeans“就没有。会不会是biobase的exprs的问题呢？感谢🙏

[hullv]

没有安装好吧？

我也遇到了这个问题。我是按照以下步骤进行安装的：
BiocManager::install("ComplexHeatmap",force = TRUE)
BiocManager::install("clusterProfiler",force = TRUE)
BiocManager::install("TCseq",force = TRUE)
BiocManager::install("Mfuzz",force = TRUE)
BiocManager::install("monocle",force = TRUE)
devtools::install_github('cole-trapnell-lab/monocle3',force = TRUE)
install.packages("circlize",force = TRUE)
devtools::install_github("junjunlab/ClusterGVis",force = TRUE)

但是，我在创建对象的时候依旧有报错：

cm <- clusterData(exp = result,

•               cluster.method = "mfuzz",
  

•               cluster.num = 9)
  

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'assayData' in selecting a method for function 'ExpressionSet': cannot coerce type 'builtin' to vector of type 'any'

str(result)
'data.frame': 14751 obs. of 5 variables:
$ Neonatal : num 11.5 12.3 12.5 10.7 12.1 ...
$ Young : num 11.4 12 12.7 10.6 12 ...
$ Middle_early: num 11.5 12.1 12.8 10.6 12.1 ...
$ Middle_late : num 11.5 12.3 12.5 10.6 12.1 ...
$ Old : num 11.6 12.3 12.5 10.6 12.1 ...

请问俊俊大神这个问题应该如何解决？

[junjunlab]

我这里确实没问题，刚从github下载的，你们看看sessionInfo：

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] tcltk     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DynDoc_1.82.0       Biobase_2.64.0      BiocGenerics_0.50.0 widgetTools_1.82.0  ClusterGVis_0.1.2  

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.34.0 circlize_0.4.16             shape_1.4.6.1              
 [4] rjson_0.2.21                httr2_1.1.0                 GlobalOptions_0.1.2        
 [7] lattice_0.22-6              vctrs_0.6.5                 tools_4.4.1                
[10] generics_0.1.3              stats4_4.4.1                parallel_4.4.1             
[13] tibble_3.2.1                proxy_0.4-27                fansi_1.0.6                
[16] cluster_2.1.6               pkgconfig_2.0.3             Matrix_1.7-0               
[19] RColorBrewer_1.1-3          S7_0.2.0                    S4Vectors_0.42.1           
[22] lifecycle_1.0.4             GenomeInfoDbData_1.2.12     stringr_1.5.1              
[25] compiler_4.4.1              codetools_0.2-20            ComplexHeatmap_2.20.0      
[28] clue_0.3-65                 GenomeInfoDb_1.40.1         class_7.3-22               
[31] pillar_1.9.0                crayon_1.5.3                SingleCellExperiment_1.26.0
[34] DelayedArray_0.30.1         iterators_1.0.14            abind_1.4-8                
[37] foreach_1.5.2               tidyselect_1.2.1            digest_0.6.37              
[40] stringi_1.8.4               purrr_1.0.2                 reshape2_1.4.4             
[43] dplyr_1.1.4                 grid_4.4.1                  colorspace_2.1-1           
[46] cli_3.6.3                   SparseArray_1.4.8           magrittr_2.0.3             
[49] S4Arrays_1.4.1              utf8_1.2.4                  e1071_1.7-16               
[52] withr_3.0.1                 UCSC.utils_1.0.0            rappdirs_0.3.3             
[55] XVector_0.44.0              httr_1.4.7                  matrixStats_1.3.0          
[58] png_0.1-8                   GetoptLong_1.0.5            tkWidgets_1.82.0           
[61] GenomicRanges_1.56.1        IRanges_2.38.1              doParallel_1.0.17          
[64] rlang_1.1.4                 Rcpp_1.0.13                 glue_1.7.0                 
[67] coro_1.1.0                  rstudioapi_0.17.0           jsonlite_1.8.8             
[70] plyr_1.8.9                  ellmer_0.1.0.9000           R6_2.5.1                   
[73] Mfuzz_2.64.0                MatrixGenerics_1.16.0       zlibbioc_1.50.0            
> 

[hullv]

我通过先加载两个包解决了这个问题。
library(Biobase)
library(Mfuzz)

[xiahui625649]

您好，我试着重新安装了几次， 但是用cluster.method=“mfuzz“ 就会有同样的报错 （Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘exprs’ for signature ‘"ExpressionSet）， 如果用”kmeans“就没有。会不会是biobase的exprs的问题呢？感谢🙏

`> cm <- clusterData(exps,

•               cluster.method = "mfuzz",
  

•               cluster.num = 8)
  

[1] "0 genes excluded.\n"
Error: unable to find an inherited method for function ‘exprs’ for signature ‘x = "ExpressionSet"’`我也遇到同样问题，请问解决了吗？

[yinyeya]

I noticed that the error occurs because the exprs function is defined in both the Biobase and ClusterGVis packages, causing a conflict when loading the ClusterGVis environment.

> find("exprs")
[1] ".conflicts"          "package:Biobase"     "package:ClusterGVis"

The mfuzz package relies on the exprs function from Biobase but does not explicitly specify it using ::.

To resolve this, I used the conflicted package with conflict_prefer("exprs", "Biobase") before running clusterData.

Alternatively, reordering the package load order (loading Biobase last) could prioritize its exprs function, like @hullv suggested, since the order of package loading determines which function takes precedence. But this approach did not work in my environment.