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P value signficancy

I need a suggestion, I analyzed a GEO data set by GEO2R. Where I found 4435 gene that are significant for adj.p.value. I want to find out the upregulated and down regulated gene from that. So how can I find that? Moreover I gave adj.p.value <0.05.If I give the range <0.01,so will I get more significant gene for that?

geo geo2r
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updated by Ram Ram • written by fahim • fahim

Moreover I gave adj.p.value <0.05.If I give the range <0.01,so will I get more significant gene for that?

You could have had your answer much faster by doing it rather than asking here.

Smaller p-values mean more stringent conditions, so let's just say that you will not get a larger number of genes than what you already have.

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updated by Ram Ram • written by Mensur Dlakic Mensur Dlakic

1 answer

I want to find out the upregulated and down regulated gene from that. So how can I find that?

Please refer to the log [base 2] fold change (log2fc):

  • negative log2fc, down-regulated
  • positive log2fc, up-regulated

Moreover I gave adj.p.value <0.05.If I give the range <0.01,so will I get more significant gene for that?

Yes, indeed. Better to say 'statistically significant', though.

Kevin

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updated by Ram Ram • written by Kevin Blighe Kevin Blighe

Thanks a lot for the suggesstion

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written by fahim • fahim

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