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vertesy / Seurat.CBE.issues

Issue tracker repo for running Seurat on CLIP/CBE
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Error in differential gene expression – replacement has 0 rows #9

Closed vertesy closed 3 years ago

vertesy commented 3 years ago 
> if (TRUE) source('~/GitHub/Packages/Seurat.pipeline/elements/Differential.gene.expression.Loop.R'); create_set_Original_OutDir()
[1] "All files will be saved under the original OutDir:  ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/"
[1] "Differential.Gene.expression"
[1] "All files will be saved under 'NewOutDir':  ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/Differential.Gene.expression/"
[1] "ParentDir was defined as: ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/"
[1] "ParentDir will be: ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/"
[1] "Call *create_set_Original_OutDir()* when chaning back to the main dir."
[1] "Resolutions analyzed:  0.2 0.5"
[1] "All files will be saved under 'OutDir':  ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/Differential.Gene.expression/res.0.2/"
Calculating cluster 0
Calculating cluster 1
Calculating cluster 10
Calculating cluster 11
Calculating cluster 2
Calculating cluster 3
Calculating cluster 4
Calculating cluster 5
Calculating cluster 6
Calculating cluster 7
Calculating cluster 8
Calculating cluster 9
4987.281 sec elapsed
Error in `$<-.data.frame`(`*tmp*`, "combined.score", value = numeric(0)) :
  replacement has 0 rows, data has 7937
vertesy commented 3 years ago

The old "avg_logFC|avg_log2FC" bug in Add.DE.combined.score.