Question: Differential expression analysis of normalized expression of RNA seq data
0
gravatar for Javad
2.1 years ago by
Javad120
Javad120 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 • 1.4k views
ADD COMMENTlink modified 2.1 years ago by Benn8.0k • written 2.1 years ago by Javad120
1

Normalized by what method? Are there replicates?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by ATpoint39k
1

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

ADD REPLYlink written 2.1 years ago by ejm32440
0
gravatar for Benn
2.1 years ago by
Benn8.0k
Netherlands
Benn8.0k 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 2.1 years ago • written 2.1 years ago by Benn8.0k
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