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Old 07-07-2013, 11:50 PM   #1
wilson90
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Location: Singapore

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Default Determine Top 100 Differentially Expressed Genes

Dear all,

I am wondering if we decide the top 100 differentially expressed genes based on:
A) Log Fold Change or
B) P-value
C) Or a combination them? (In the case, order matters? (logFC first, p-value?)

Thank you.

Best Regards,
Wilson
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Old 07-08-2013, 04:53 AM   #2
sisch
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Default

I'm not sure that it makes sense to look only at the top hundred of differentially expressed genes from a statistical point of view. Either they are significantly different or not.
However, if you want to sort your data a bit, I would suggest the following:

1. Determine differential expression by statistics (whatever test you see fit)
2. From the set of significantly differing genes, sort by fold-change (or log-fold-change)

This way you get a list that has on top the most differing (in terms of expression) genes that are confirmed to be differential by statistics.

Still, looking only at a subset of results that came out of a statistical test as significant feels wrong.
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