I am trying to run DESeq2 with featureCounts files from a single cell sequencing project. I have 8 different samples, so 8 collections of tabular files. Each file has a column with Geneid and a column with the count. When I try to run DEseq (4 samples from one group vs 4 samples in another group) I get an error message saying:
Error in data.frame(…, check.names = FALSE) :
arguments imply differing number of rows: 135280, 235928, 226602, 203217, 210838, 214950, 279139, 133575
Calls: get_deseq_dataset … eval → eval → eval → cbind → cbind → data.frame
The report also states that:
The tool was executed with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices.
How can I resolve this?