Question

Differential expression analysis using GFOLD and DESeq2

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5.5 years ago

newbio17 ▴ 360

Details about the experiment can be found on bioconductor page below:

The author of DESeq2 mentioned that I cannot get analysis results for interaction between type and time due to the number of samples.

Since GFOLD is specifically designed for doing analysis without replicates, could I present results from GFOLD for differential expression between type and time interaction alongside with DESeq2 results?

Thank you.

RNA-Seq deseq2 gfold • 1.3k views

ADD COMMENT • link updated 5.5 years ago by Kevin Blighe 87k • written 5.5 years ago by newbio17 ▴ 360

score 3 · Accepted Answer · 2018-10-23

Sure you can, but just be very clear about how you derived the different statistical values. Be as 'brutally honest' about your analysis as you possibly can, and be prepared for criticism. For one, I would never give much credibility to comparisons containing just a single sample. There may be logical reasons why you have not been able to increase your sample n, though.

Kevin