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update docs
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GEHoffman committed Jan 23, 2024
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Expand Up @@ -148,7 +148,18 @@ attr(res.dl[[clustID]])[1:2]


# Errors at the cluster level
Some model failures affect every gene in an assay. `dreamlet()` tests an initial model fit before analysis of each gene. If the initial fit fails for a cell cluster, then `details(res.dl)$error_initial` will be `TRUE`.
Some model failures affect every gene in an assay. `dreamlet()` tests an initial model fit before analysis of each gene. If the initial fit fails for a cell cluster, then `details(res.dl)$error_initial` will be `TRUE`. Details of the errors can seen with
```{r err, eval=FALSE}
seeErrors(res.dl, initial=TRUE)
# the most common error is:
"Some predictor variables are on very different scales: consider rescaling"
```
This indicates that the scale of the predictor variables are very different and can affect the numerical stability of the iterative algorithm. This can be solved by running `scale()` on each variable in the formula:
```{r formula, eval=FALSE}
form = ~ scale(x) + scale(y) + ...
```




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