Question: Differential expression analysis of normalized expression of RNA seq data
0
gravatar for Javad
18 months ago by
Javad90
Javad90 wrote:

Dear All,

I have a normalized expression table of RNA seq data. I normally use DESeq2 but it needs raw count table not normalized data. Which R package I can use to analyse a Normalised table?

Best,

rna-seq • 936 views
ADD COMMENTlink modified 18 months ago by Benn7.9k • written 18 months ago by Javad90
1

Normalized by what method? Are there replicates?

ADD REPLYlink modified 18 months ago • written 18 months ago by ATpoint29k
1

This post from the bioconductor support site maybe of help: https://support.bioconductor.org/p/56275/

ADD REPLYlink written 18 months ago by ejm32440
0
gravatar for Benn
18 months ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

None. There is no package that is able to do (sound) statistical analysis of normalized RNAseq data. Get read count data, and do what you normally do with DEseq2 or limma voom, etc.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Benn7.9k
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