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aec
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@aec-9409
Last seen 4.4 years ago
Dear all,
I run DESeq2_1.18.1 with default options and obtained odd results. The significant transcripts (FDR<5%) are due to one or two outlier samples.
I checked the expression values and all samples except the outliers have 0 counts,
How can I deal with this situation? Which parameters should I modify? changing Cook's distance? disable independent filtering?
Thanks,
Hi Michael,
I have 20 samples, 10 per group ( I think DEseq2 requires minimum of 7 for outliers).
and the normalized counts of 2 significant genes:
they appear to be high enough...
It's hard to say for a given gene why filtering/replacement does or does not apply, because it depends also on the dispersion of all the other genes. Nevertheless, the above code should help you here.
Yes, the above code helped me, but still, I do not understand why DESeq2 is not able to deal with these cases with default options.