[R] Normalize GEO Data

[Ebert,Timothy Aaron]

One approach for adjusted p-values is to divide by the "magic cut-off" value by the number of tests. Typically one decides significance if the p-value is lass than 0.05. So not it is 0.05/(number of tests). This can be too conservative, but sometimes there are not many options. If you have a multiple comparison procedure (like the mean difference between five treatments) then there are tests like Tukey's HSD test, and many others that try for more balance.

"They are all 1" is possible but unlikely that all p-values would equal 1 except for one vale of 0.636. Maybe some data was not copied correctly, or maybe the model was not built correctly, or data not read in correctly. Please check that the data the computer has in memory matches the data in your file

Tim

-----Original Message-----
From: R-help <r-help-bounces using r-project.org> On Behalf Of Anas Jamshed
Sent: Monday, August 15, 2022 11:34 AM
To: R-help Mailing List <r-help using r-project.org>
Subject: [R] Normalize GEO Data

[External Email]

I performed GEO2R analysis on a series dataset and I'm looking to find the up-regulated and down-regulated genes. I know that to find up-regulated and down-regulated genes, I should check logFC (Fold-change in log2 scale (generally)).Consider the value of 1 in log2 is 0. There is optimal cutoff but log2 > 1 indicates up-regulation and log2 < -1 indicates down-regulation of genes. Moreover, I should consider adj.p.val which is the adjusted p-value (corrected p-value dues multiple comparisons). Again there is no generally accepted cutoff but I should consider values < 0.05 which indicates the test is statistically significant.
But the problem is in this particular GSE series none of the adj.p.value is < 0.05 - they are all "1" and a "0.636". However, the logFC values are >1, but none of the samples have a condition of "p <0.05 & logFC > 1".
So, can it be said that in this case, I need to normalise my data to find out the DEGs, up-regulated and down-regulated genes in a series GEO file?

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