Question: NAs create inaccuracies with BH corrections in deseq2
0
gravatar for marc.osullivan
10 weeks ago by
marc.osullivan0 wrote:

I've just started using deseq2 and have noticed that some p adjusted values are appearing as NA in my output CSV. The issue with this is the package excludes any genes with an adjusted p-value = NA from the total ranking count and therefore generates an inaccurate adjusted p-value.

i.e. total genes measured = 520

genes with adjusted p-value = 0.000etc, n = 480

genes with adjusted p-value = NA, n = 40

Example where genes with adjusted P-value = NA are excluded: Most significantly altered gene, p-value = 0.0001, adj.p-value = 0.0001*(480/1)=0.048

Example where genes with adjusted P-value = NA is included: Most signigicantly altered gene, p-value = 0.0001,adj.p-value = 0.0001*(520/1)=0.052

Should we not still include all genes that had read counts in the total ranking for a correct BH adjustment?

deseq2 • 79 views
ADD COMMENTlink modified 10 weeks ago by Michael Love22k • written 10 weeks ago by marc.osullivan0
Answer: NAs create inaccuracies with BH corrections in deseq2
2
gravatar for Michael Love
10 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

This is discussed in the vignette and the DESeq2 paper. You can also read about IHW which is a more sophisticated approach.

ADD COMMENTlink written 10 weeks ago by Michael Love22k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 83 users visited in the last hour