Hello, I am doing DESeq on my RNA-Seq data. However, I have filtered my conditions individually based on the replicates within each condition. Basically, I have 5 conditions with 5 replicates. I filtered each condition based on the rowmeans of the replicates (5 and above reads are kept). However, now that I am doing DESeq, it does not allow me to make a DESeq set or do any sort of comparisons
I receive this error every time. This is likely due to the fact that none of my conditions have the same lengths due to the prefiltering.
longer object length is not a multiple of shorter object lengthError in Ops.factor(a$V1, l[]$V1) : level sets of factors are different
I have been using DESeqDataSetFromHTSeqCount within the DESeq2 R package, with each replicate file having separate text files with gene names and counts.
Is there any way for me to remove the genes that are simply not shared between all of the conditions or do the comparison without regards to any genes that are only present in certain conditions? Thank you!