Normalize GEO Data

I have no idea what you mean. Please do *not* respond to me privately.

On Mon, Aug 15, 2022 at 9:48 AM Anas Jamshed <anasjamshed1994 at gmail.com>
wrote:

but how can I apply for RMA?

On Mon, Aug 15, 2022 at 9:45 PM Bert Gunter <bgunter.4567 at gmail.com>

wrote:

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.

Cheers,
Bert

On Mon, Aug 15, 2022 at 8:34 AM Anas Jamshed <anasjamshed1994 at 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?

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