Question: Filtering the gene list using q-value instead if p-value
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gravatar for vasanth.m.29
20 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 • 510 views
ADD COMMENTlink modified 20 months ago by Devon Ryan92k • written 20 months ago by vasanth.m.290
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gravatar for Devon Ryan
20 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k 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 20 months ago by Devon Ryan92k

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

ADD REPLYlink written 20 months ago by vasanth.m.290

Google "adjusted p-value"

ADD REPLYlink written 20 months ago by Devon Ryan92k
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