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some questions about GoMiner

some questions about GoMiner - Bioinformatics

some questions about GoMiner - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 09-10-2008, 01:43 AM
Pipette Filler
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Default some questions about GoMiner



HI everyone I am quite new to GO analyze, and I use GoMiner to do it, but I don`t
understand the results very well. could you please explain it for me?
there is a example result below:

GO ID Total Under Over Change P-Value (Under) P-Value (Over) P-Value (Changed) FDR (Under) FDR (Over) FDR (Changed) Term
0005662 1 0 0 1 1.0000 1.0000 1.0000 0.0000 0.0000 1.0000 DNA replication factor A complex
0016591 1 0 0 1 1.0000 1.0000 1.0000 0.0000 0.0000 1.0000 DNA-directed RNA polymerase II, holoenzyme

could you please tell the mean of the P-value?
thanks
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Old 09-17-2008, 06:35 AM
Pipette Filler
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Default Re: some questions about GoMiner

Hi,

I'm not an specialist in biostatistics but I've been using GoMiner to interpret MA results. In this case P-values are related to the level of confidence for which your changes in gene expression can be associated to the GO groups. Those groups with P-value <= 0.05 (typical cutoff) represent statistical significant groups meaning that you should concentrate on those groups in your analysis. The best way is to load the table in Excel or some similar program, and sort the rows by ascending order using for example the "P-Value (Changed)" column. You can also filter the rows to see just those groups with "P-Value (Changed)" less than or equal to 0.05.

Regards.-
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