Question: DeSeq2 rlog or varianceStabilizingTransformation using ouput file
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gravatar for BM
2.1 years ago by
BM40
United Kingdom
BM40 wrote:

I have a DeSeq2 output file generated by an external RNA-seq. So the output is the usual has the usual columns: gene identifiers, baseMean, log2FoldChange, lfcSE stat, pvalue, padj. However, I want to perform rlog or varianceStabilizingTransformation on my data. Is there a way to do this transformation just using the output file above? When I go back and perform the DeSeq2 analysis on my counts, there are differences between my output and the one given to me by the company. So I would like to use the output file.

ADD COMMENTlink modified 2.1 years ago by WouterDeCoster37k • written 2.1 years ago by BM40

It all depends on the model that was used by the external collaborator and the design they have implemented while performing the DE analysis. You can simply ask them how they did and implement the same on your counts and see how are the end results comparable. Or ask them to perform the way you are performing the analysis to the counts (if that is possible). The motivation of the models depends on various factors and the design of the experimental matrix in the DESEQ2 design model. You cannot use an external collaborator output to trace back the counts data from DESeq2 since am guessing your counts data might not be exact integer and also depends on what rounding was applied before feeding the counts to DESeq2. Hope I was clear

ADD REPLYlink written 2.1 years ago by ivivek_ngs4.7k
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gravatar for WouterDeCoster
2.1 years ago by
Belgium
WouterDeCoster37k wrote:

No, that's not possible. The output with differentially expressed genes doesn't contain the information needed to get per sample normalized expression levels.

ADD COMMENTlink written 2.1 years ago by WouterDeCoster37k
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