Dear Dr. Anders,

I am using DESeq package for doing the differentially expressed analysis of
miRNA in two conditions (case and control) without replicate.

When I run estimateSizeFactors() function, the result of sizeFactors(cds) is
1 and 1 for both conditions.

1- Is it normal to have same sizeFactors for both conditions?

2- This function use for normalization of raw data, right? Or I should
normalize the data before using the package?



Actually I run the following code:


library(DESeq)

countsTable=read.table(file="Con12Raw.txt", sep="\t",
header=T);head(countsTable)
rownames(countsTable)=countsTable$SeqName
countsTable=countsTable[,-1]
head(countsTable)
conds<-c("N","T")
cds=newCountDataSet(countsTable,conds)
cds=estimateSizeFactors(cds);sizeFactors(cds)
cds <- estimateVarianceFunctions( cds , method="blind")
res <- nbinomTest( cds, "N", "T" )
head(res)
plot(res$baseMean, res$log2FoldChange,
col=ifelse(res$pval<0.05,"red","black"), log="x",pch=16,cex=1)
abline(h=0, col="green")
write.table(res, file="DesCon12Raw.txt", sep="\t",row.names = FALSE)



Many thanks in advance for your reply and help



-- 
Kind regards,
Sara

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