This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to read multiple samples with DESeq2?

Hello

I have a count file which has multiple columns, (one column for one sample). As I found, In DESeq2 we should insert count files separately.

Is it possible to insert one file with multiple columns? like below:

Gene    Sample1  Sample2

g1      22       0

g2      5        60

....

Thanks

rna-seq r deseq2
• 2,993 views • link
updated by ivivek_ngs ivivek_ngs • written by mirzaei86.vahid • mirzaei86.vahid

3 answers

see "Starting from count matrices" in this document http://www.bioconductor.org/help/workflows/rnaseqGene/

• 0 views • link
written by Santosh Anand Santosh Anand

Have you looked at the DESeq2 vignette (specifically section 1.3.3)?

• 0 views • link
written by GenoMax GenoMax

DESeq2 vignette should be fine. However , it actually needs your knowledge in R rather than the tool you want to use for DE analsys or whatever your are aiming to dol.

Read the vignette well as suggested by others. Then the below guidlines should work if you understand from the vignette. Read the file in R with header=T and rownames=1. Create the colData dataframe with the condition or group you have for your experiment Then create the DESeq data object with the design. In your case it should be DESeqDataSetFromMatrix function

• 0 views • link
written by ivivek_ngs ivivek_ngs

Log in to answer this question.

More posts like this