I mean how can I apply RMA to my datasets? On Mon, Aug 15, 2022 at 9:50 PM Bert Gunter <bgunter.4...@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 <anasjamshed1...@gmail.com> > wrote: > > > > but how can I apply for RMA? > > > > On Mon, Aug 15, 2022 at 9:45 PM Bert Gunter <bgunter.4...@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 <anasjamshed1...@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]] > >> > > >> > ______________________________________________ > >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> > https://stat.ethz.ch/mailman/listinfo/r-help > >> > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > >> > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
