Question: DESeq possible when only rlog table available? (DESeq2 package)
0
gravatar for sreibe
19 months ago by
sreibe0
sreibe0 wrote:

Hi there,

I tried to re-analyse RNA-seq data that was made available on GEO and referred to in a publication.

However, the only "raw" data that was made available was the rlog table extracted from assay(rld) (at least that's what I understand from the labeling of the provided table).

Is there any way to feed this table with rlog values into the DESeq function and defining the groups I want to compare?

Or would I need the raw count table to actually re-do the analysis? I would assume so, but I wanted to double-check.

Many thanks

Saskia

 

 

deseq deseq2 rlog • 277 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by sreibe0
Answer: DESeq possible when only rlog table available? (DESeq2 package)
1
gravatar for Wolfgang Huber
19 months ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

You need the raw counts to exactly reproduce the DESeq2 analysis. There is no easy way back from the rlog counts.

You could try ordinary t-tests, linear models or limma on the rlog-data. The results should be similar (depending on data quality), but will not be the same.
 

ADD COMMENTlink written 19 months ago by Wolfgang Huber13k
Answer: DESeq possible when only rlog table available? (DESeq2 package)
0
gravatar for sreibe
19 months ago by
sreibe0
sreibe0 wrote:

Thanks Wolfgang, I thought so, I just wanted to make sure before I might mention to them that they did not provide raw data and therefore make it impossible to reproduce their results.

Cheers

Saskia

ADD COMMENTlink written 19 months ago by sreibe0
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