Question: RNAseq tximport Deseq2
0
gravatar for tanyabioinfo
17 months ago by
tanyabioinfo20
tanyabioinfo20 wrote:

 

HI

I am using the tximport module to process the output of Salmon. Then I am using the vst(dds) to normalise the data. I understand that the assay for dds is count. How can I process the abundance(TPM) using the vst so that my TPM data is normalised. 

My R code looks:

txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE)
sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time))
rownames(sampleTable) <- colnames(txi$counts)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition+time)

vsd <- vst(dds) 

deseq2 tximport • 337 views
ADD COMMENTlink modified 17 months ago by Michael Love23k • written 17 months ago by tanyabioinfo20

I missed this post because the tags were not separated, so didn’t get an email alert.

ADD REPLYlink written 17 months ago by Michael Love23k
Answer: RNAseq tximport Deseq2
1
gravatar for Michael Love
17 months ago by
Michael Love23k
United States
Michael Love23k wrote:

The VST is only designed for counts. We recommend using variance stabilized, transformed counts for downstream applications like visualization, distances, clustering or classification/prediction methods that benefit from homoskedastic data.

TPM is useful for comparing abundance across transcripts or genes. It should be proportional to the true abundance of RNA molecules.

ADD COMMENTlink written 17 months ago by Michael Love23k
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