Hi,

I am very new to DESEQ2 and I am struggling to create the initial Deseq2 dataset. I have a zip file with HT-seq counts for 5 days and each has a certain number of repeats, there are 22 files in total in the zip file. Each with the counts from each studied day. I don't understand how to get this into a format to where I can do differential analysis across all days to find out which day a certain gene I am looking at has the highest significant expression or differentially expressed.

This is what I've found online so far:

sampleFiles <- grep("D",list.files(directory),value=TRUE)

so this identifies which files I want

sampleCondition <- sub("(.*D06,*D13).*","\\1",sampleFiles)

then I want the conditions to be the days but I can't get this code to do that?

sampleTable <- data.frame(sampleName = sampleFiles,
                          fileName = sampleFiles,
                          condition = sampleCondition)
sampleTable$condition <- factor(sampleTable$condition)

I would really appreciate any help I'm very lost with this

thank you!!

Hi Chloe, it may help to add more information. For example, showing the contents of sampleTable, and also the contents of one of the raw count files.

You indicate that you have HT-seq count files, and it looks like you have already been following the vignette: htseq-count input. Can you try the next step involving DESeqDataSetFromHTSeqCount()?; then proceed from Differential expression analysis.

Kevin