DE fold change calculation issue
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7.4 years ago
cecilin92 ▴ 10

I have a edgeR results table linked to sample expected count values, but a question confused me a lot. Someone please just give me a simple explanation of how the number under A1, A2, A3, B1, B2 and B3 relate to the raw read numbers? For this given gene, the expect count may be (0,0,0 vs 5.7, 2.31,1.24) and the fold change is 1444.89x and the FDR is extreme small. Do I trust this? Thanks a lot!

Here is the example,

id               Accession Version     Fold change     logFC     FDR          A1     A2     A3     B1      B2       B3
c78690_g3_i1     XP_007258149.1        1444.89         10.50     2.05E-16     0      0      0      5.7     2.31     1.24
expected-count edgeR RNA-Seq • 2.4k views
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Are you expecting a different answer than the one I gave you here?

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No sir, I did appreciate your answer which help me a lot. Besides, I am wondering how the zero situation calculated but did not found in the tutorial. In SEQanswers someone gave a answer that adds a pseudocount of 0.125 to all observations, do you have any idea about this issue?

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Yeah, I'd forgotten about that. It's the prior.count option.

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Thank you. Thanks to you the edgeR seems to be easier for me. Then I will dig out the calculation method behind prior.count.

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One more question, based on such zero values, can I still trust in this differently expressed gene (for publishing)?

Thank you!

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For this example I would be hesitant. The reason for this is that the counts in group B are still pretty low, so it's tough to gauge if this is really just noise. In any case, you should be validating some of the findings in independent samples with a different technology if the exact candidates are important (rather than if just changed pathways are important...in which case you'd then validate the pathway).

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