DESeq2 log2 fold change
0
5
Entering edit mode
4.3 years ago
bioinfonerd ▴ 80

Hi everyone,

I did the DESeq2 on my Nanostring gene expression data using the below code:

dds <- DESeqDataSetFromMatrix(countData = counts_set,colData = annotation,design = ~ pt_id+treatment)
sizeFactors(dds)  <- estimateSizeFactorsForMatrix(counts(dds))
dds <- DESeq(dds)
res <- results(dds,contrast=c("treatment","Treatment","Vehicle"))

But the log2FC I am getting are quite different from the log2FC I calculated manually. Could you let me know if that is normal and correct?

Thanks!

Nanostring deseq2 • 6.7k views
ADD COMMENT
0
Entering edit mode

I guess that your FCs for the genes with smaller couts are much larger than the DESeq2-ones?

EDIT: You should have a look at this post from the DESeq2 developer towards DESeq2 on Nanostring data. He is concerned that the normalization might be a problem.

ADD REPLY

Login before adding your answer.

Traffic: 1563 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6