Question

rlog value changed with the same input count matrix between 2015 and 2017

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Yang_Zheng_Neuro • 0

@yang_zheng_neuro-14279

Last seen 5.0 years ago

HMS

Hi,

I've been back and forth analyzing my RNA-sequencing data.

I noticed that with the same input dataset (counts and meta), the rlog transformed data generated in Jan 2017 (DESeq2 1.14.1) are different from the one I generated before (I did not record which version of the DESeq2 package I was using in 2015). I'm pretty sure that I did the exact same thing but the versions of the DESeq2 packages.

I'm wondering what's changed in the algorithm.

I appreciate your help in advance!

deseq2 • 449 views

ADD COMMENT • link updated 6.5 years ago by Michael Love 41k • written 6.5 years ago by Yang_Zheng_Neuro • 0

score 0 · Answer 1 · 2017-10-27

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Michael Love 41k

@mikelove

Last seen 22 hours ago

United States

The transformations rely on the dispersion estimates, and depending on what was the older version, the algorithm for finding the dispersion values changed slightly.

ADD COMMENT • link 6.5 years ago Michael Love 41k

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Hi Michael,

Thank you very much for your response.

I was also able to find similar questions elsewhere and of course your answers that are super helpful.

Thank you again.

ADD REPLY • link 6.5 years ago Yang_Zheng_Neuro • 0