[R] Normalize GEO Data

Bert Gunter bgunter@4567 @end|ng |rom gm@||@com
Mon Aug 15 18:44:51 CEST 2022

You realise, I presume, that your sample size may be too small to flag
*any* genes, up or down, using p-values? ... and that at a more
fundamental level, the use of hypotheses tests and p values for any of
this is controversial? A discussion of the latter is wayyyyyy off
topic on this list, but if you care to go down that rabbit hole,
online searches should take you there.


On Mon, Aug 15, 2022 at 8:34 AM Anas Jamshed <anasjamshed1994 using gmail.com> wrote:
> 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?
>         [[alternative HTML version deleted]]
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