Thank you for the responses so far! The idea behind this is that I don’t want to limit users to a certain DGE toolkit, may it be DESeq2, edgeR or frameworks specifically developed for single cell data such as muscat. I’d like to have a common structure that users can pour their results into (most variables are probably generated by all methods), which ensures that it matches a certain format. Then, I can build the visualisation in a Shiny app around that format. I could just make my own format but I want to avoid complicated explanations of how the data frame must look like to be in the correct format. Also, knowing myself, if I have control over the format, I might get tempted to change it in the future resulting in compatibility issues...
Regarding the SummarizedExperiment class: Would you suggest leaving most of the object empty and use the feature info slot (accessible through “rowData()”)? From the vignette it looks like that's just a normal data frame. I’ll keep exploring. Best, Roman > On 9. Mar 2020, at 13:02, Constantin Ahlmann-Eltze > <constantin.ahlm...@gmail.com> wrote: > > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
