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

Question

[vasanth.m.29]

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?

Answer 1

[Devon Ryan]

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.

[vasanth.m.29]

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

[Devon Ryan]

Google "adjusted p-value"