DESEQ2 application on control vs treatment

Question

[bioinfonerd]

enter code hereHi everyone,

I have 5 control samples and 5 treatment samples for the same patients and I would like to extract the differentially expressed genes between control and treatment samples.

The method I am using now is:

dds <- DESeqDataSetFromMatrix(countData = counts_set,colData = annotation,design = ~ condition)
dds <- DESeq(dds)
res <- results(dds,contrast=c("condition","Treatment","Vehicle"))

where condition represent control and treatment as follows:

        condition
01_C   Vehicle
02_C   Vehicle
03_C   Vehicle
04_C   Vehicle
05_C   Vehicle
01_T Treatment
02_T Treatment
03_T Treatment
04_T Treatment
05_T Treatment

Could you please let me know if this is a correct way to do?

Thanks

[Ram]

I've split your tag into two keywords: nanostring and deseq. That will make them more relevant.

[bioinfonerd]

Thanks very much!!!!!

Answer 1

[h.mon]

It seems correct, except for the fact you say you have 5 control and 5 treatment samples, whereas your condition variable has 10 control and 10 treatment samples.

[bioinfonerd]

Thanks!! I have corrected it.

[Kevin Blighe]

The code does indeed look fine - good work. Please also take time to look through the Vignette at the part where it discusses the results object.