P value signficancy

Question

[fahim]

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?

[Mensur Dlakic]

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.

Answer 1

[Kevin Blighe]

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

[fahim]

Thanks a lot for the suggesstion