[R] Normalize GEO Data

[Anas Jamshed]

I mean how can I apply RMA to my datasets?

On Mon, Aug 15, 2022 at 9:50 PM Bert Gunter <bgunter.4567 using gmail.com> wrote:

> 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 using gmail.com>
> wrote:
> >
> > but how can I apply for RMA?
> >
> > On Mon, Aug 15, 2022 at 9:45 PM Bert Gunter <bgunter.4567 using 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 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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> >> > and provide commented, minimal, self-contained, reproducible code.
>

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