Question: what is the best method (normalization) to compare RNA-Seq samples from different labs
gravatar for RS
19 months ago by
RS0 wrote:


I have more than 100 RNA-Seq samples (files) from different labs (i.e, different papers) for plant tissues. I want to compare them (for DEGs, PCA, tSNE, absolute expression, etc.). But for this, the data should be normalized. Data are from different labs, thus I want to take special care for the normalization which can remove any bias. I know the bias may depends on many factors. But here as a first step, I want to know what kind of normalization should be applied to the single count data (matrix)? I guess TMM is one of the best normalization technique in this scenario. Is there any other pipeline for this kind of task? and lastly, can I just compare the data with TPM values in doing PCA and tSNE?

Thanks for help!


ADD COMMENTlink modified 19 months ago by Dattatray Mongad350 • written 19 months ago by RS0
gravatar for Dattatray Mongad
19 months ago by
National Centre for Cell Science, Pune
Dattatray Mongad350 wrote:

Yes you can do PCA using TPM values and TMM has been widely used as normalization technique for transcriptome data. You can use DESeq2

ADD COMMENTlink written 19 months ago by Dattatray Mongad350
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