How to extract the results table for specific samples names after normalization by DESeq in R?

Question

[Amr]

How to extract the results table for specific samples names after normalization by DESeq in R?

After I did normalization in R with DESeq2 I got the results table with results function, now I need to get the results but not for all samples, I just need for 2 samples, how to extract it?

res <- results(dds)
res

log2 fold change (MLE): condition Normal Cell vs Cancer Cell

Thanks in advance

Answer 1

[Amr]

I guess the best solution for this question is:

countdata3<- subset(countdata, select=c("sample_name1_rep1", "sample_name1_rep2", sample_name2_rep1","sample_name2_rep2"))

coldata3<- data.frame("condition"=as.factor(c(rep("Normal",2),rep("Mutated",2))),row.names=colnames(countdata3))

dds3 <- DESeqDataSetFromMatrix(countData = countdata3, colData =coldata3,design = ~condition )

dds3 <- DESeq(dds3)

results(dds3)

Then the results will be calculated depending on the samples inside the dataframe not all samples.

[andres.firrincieli]

How to extract the results table for specific samples

You are not "extracting" the result table. You are doing a completely new the deseq2 analysis with a smaller set of samples from the original dataframe (countdata)

[Amr]

Yes you are right, but is there another way to extract them after making normalization for all samples?