[R] Normalize GEO Data

[Anas Jamshed]

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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