Hi Roman, I think it is probably also helpful to check out how DESeq2 and edgeR (two popular Bioconductor packages for differential expression analysis) have solved that problem:
In DESeq2 for example the `nbinomWaldTest()` function calculates the differential expression and stores the results in the `rowData()` of the DESeqDataSet / SummarizedExperiment. The `results()` function extracts a standard `data.frame` with all the columns that you mentioned. In edgeR the `glmLRT()` function calculates differential expression with the likelihood ratio test and returns directly a `data.frame` with the mentioned columns. Best Regards, Constantin Am 09.03.20 um 12:44 schrieb Shepherd, Lori: > I would imagine a SummarizedExperiment would be the best option > https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html > > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Roman Hillje > via Bioc-devel <bioc-devel@r-project.org> > Sent: Monday, March 9, 2020 6:48 AM > To: bioc-devel@r-project.org <bioc-devel@r-project.org> > Subject: [Bioc-devel] Class for differentially expressed genes? > > Hi all, > > I was wondering if there is a class for results of differential gene > expression analysis. I couldn�t find anything generic. Perhaps it�s too > similar to a simple data frame, but I like the idea of having a consistent > format. I would imagine something that holds gene names, statistics (logFC, > p-value, adjusted p-value), plus optional information, e.g. the percent of > cells expressing a gene (in the context of scRNA-seq). This could then be > attached to an SCE object (�metadata" slot) to keep all results together. I�m > probably making things too complicated and should just use a simple data > frame but wanted to be sure that I�m not missing any existing solution. I�d > appreciate if you share your advice. Thank you! > > Cheers, > Roman > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
