This is a test version of Biostars. For the public version, visit https://www.biostars.org.
DESeq2 R package to perform RNAseq analysis

Hi Everyone, I have 3 different samples (Sample_A, Sample_B and Sample_C) and two replicates for each. So the data matrix I have contains six different columns of fold counts for Sample_A1, Sample_A2, Sample_B1, Sample_B2, Sample_C1, Sample_C2. I want to know how I can use DESeq2 tool for this data matrix and do my RNAseq analysis. Can someone please clarify. Thanks.

rna-seq
• 270 views • link
updated by h.mon h.mon • written by MAPK MAPK

1 answer

Read the section Contrasts, found at "Analyzing RNA-seq data with DESeq2".

• 0 views • link
written by h.mon h.mon

Thanks for your answer. While it says about utilizing log2 fold change of B vs A, of C vs A, and of C vs B, it does not mention about how it treats replicates. Since I have three samples but with two replicates, I am not sure how this is going to be useful.

• 0 views • link
written by MAPK MAPK

Log in to answer this question.

More posts like this