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Filtering the gene list using q-value instead if p-value

I have obtained DEG lists from Tuxedo and Kallisto with genes 515396 and 747160 respectively. Can I filter these lists based on q-value instead of p-value as both pipelines used different methods to calculate p-value?

rna-seq deglist
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updated by Devon Ryan Devon Ryan • written by vasanth.m.29 • vasanth.m.29

1 answer

At the end of the day you'll need to filter by either adjusted p-value or q value (never raw p-value) anyway, so that shouldn't be an issue. The numbers of genes (I assume transcripts) is absurdly high. For reference, the human genome has around 200000 known transcripts in the most recent annotation. I would be very hesitant to believe anything that gave you such high values.

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written by Devon Ryan Devon Ryan

Thank you very much. What do you mean by adjusting p-value or q-value. Does it mean using cut off.

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written by vasanth.m.29 • vasanth.m.29

Google "adjusted p-value"

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written by Devon Ryan Devon Ryan

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