I want to get the count matrix of genes from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it possible for GSE146049? After getting counts, I want to do TMM normalization. [[alternative HTML version deleted]]
Dear Anas Jamshed, This is a list for R, not for specific genomic question using R. You will have more chance to have answers using a genomic list. And when you ask question, it is better to not use abbreviation that only people from that field will understand: TMM ? Marc Le 02/04/2023 ? 17:09, Anas Jamshed a ?crit?:> I want to get the count matrix of genes from > https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it > possible for GSE146049? After getting counts, I want to do TMM > normalization. > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.
It's a microarray data set, so I don't think you would want to apply an RNA-seq pipeline. You'd be better off applying a normalization appropriate for this type of microarray data. HTH, Peter On Sun, Apr 2, 2023 at 11:09?PM Anas Jamshed <anasjamshed1994 at gmail.com> wrote:> > I want to get the count matrix of genes from > https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it > possible for GSE146049? After getting counts, I want to do TMM > normalization. > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.