Hi there!
I am sending you this question because we've been using DESeq for some of the analysis that we usually perform and now we'd like to jump to DESeq2. We've been checking the DESeq2 manual but it is not clear to us how to switch from one version to the other. Could you please suggest what could be a proper way?
DESeq is embedded in our pipeline and we'd like to add now version 2. The problem is that the library functions seem to have changed considerably, as there seems not to be a direct way to translate a step from one to the other, according to the guide of DESeq2.
I am adding below and example of the code that we use with DESeq:
library("DESeq")
countTable = read.table("/Analysis/deseq/Dox_vs_DMSO.csv",header=TRUE, row.names=1)
condition = factor(c("DMSO","DMSO","Dox","Dox"))
libType = c("oneFactor","oneFactor","oneFactor","oneFactor")
experiment_design=data.frame(row.names = colnames(countTable),condition,libType)
cds = newCountDataSet(countTable,condition)
cds = estimateSizeFactors(cds)
normalizedReadCounts = counts(cds,normalized=TRUE)
write.table(normalizedReadCounts,file="/Analysis/deseq/Dox_vs_DMSO.normalizedCounts.csv",row.names = TRUE,col.names = TRUE,append = FALSE, quote = FALSE, sep = "\t",eol = "\n", na = "NA", dec = )
cds = estimateDispersions(cds)
res = nbinomTest(cds,"DMSO","Dox")
write.table( res, file="/Analysis/deseq/Dox_vs_DMSO.differentialExpression.csv",row.names = TRUE,col.names = TRUE,append = FALSE, quote = FALSE, sep = "\t",eol = "\n")
Our main questions are:
1. How could we use as input file for DESeq2 a full table that contains row counts for the different samples in different columns (and not as separated files)?
2. We would like to obtain and save with DESeq2 a table with normalized counts, as we did with DESeq (please see the attached code above). Is there a way?
What function in DESeq2 could provide that? (like in DESeq normalizedReadCounts = counts(cds,normalized=TRUE)).
Basically, we would like to know how to perform similar steps with DESeq2.
Thanks a lot !!
