Question: what to do when adjusted p-values are not acceptable in RNASeq?
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gravatar for nazaninhoseinkhan
2.4 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan390 wrote:

Dear all,

I have RNASeq data of 2 normal and 5 cancer tissues.

Although the quality of reads were very good, when I run Deseq2 the adjusted p-values was not acceptable at all (only 3 genes with adjusted p- value less than 0.05).

Can you guide me how can I select differentially expressed genes in this situation?

Regards

Nazanin

rna-seq fdr • 887 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by nazaninhoseinkhan390
3

Cancer is really diverse in gene expression, could be better to analyze your cancer samples individually using the normals as "control", also you probably want to try another package as EdgeR to see if this is something particular in your dataset.

ADD REPLYlink written 2.4 years ago by JC9.5k

You can also try an integrated approach like metaseqR with more than one algorithms and combined p-values which may partially remedy your problem. Disclaimer: I am the author of that package.

ADD REPLYlink written 2.4 years ago by Panagiotis Moulos20

Take a look at the correlations between the expression levels of the cancer samples (and control). You can then exclude samples that look very different from the rest or split them into two groups (according to their similarity or type).

ADD REPLYlink written 2.4 years ago by Asaf7.0k

How are you counting the reads that map on each feature? HTSeq? If yes, how many reads you have in the "NoFeature"? Are they a large fraction of your dataset?

ADD REPLYlink written 2.4 years ago by Macspider3.0k
0
gravatar for nazaninhoseinkhan
2.4 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan390 wrote:

Dear JC, Panagiotis, Asaf and Macspider,

Thank you so much for your comments.

I re-run the Deseq2 after calculating read numbers using Htseq Count and the result was OK this time.

I realized that the first time I had introduced the Normal and Cancer groups wrongly.

I hope everything goes well with you

Nazanin

ADD COMMENTlink written 2.4 years ago by nazaninhoseinkhan390
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