Question: Filtering the gene list using q-value instead if p-value
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gravatar for vasanth.m.29
3 months ago by
vasanth.m.290 wrote:

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 • 158 views
ADD COMMENTlink modified 3 months ago by Devon Ryan80k • written 3 months ago by vasanth.m.290
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gravatar for Devon Ryan
3 months ago by
Devon Ryan80k
Freiburg, Germany
Devon Ryan80k wrote:

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.

ADD COMMENTlink written 3 months ago by Devon Ryan80k

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

ADD REPLYlink written 3 months ago by vasanth.m.290

Google "adjusted p-value"

ADD REPLYlink written 3 months ago by Devon Ryan80k
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