[Bioc-devel] Class for differentially expressed genes?

[Constantin Ahlmann-Eltze]

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-bounces using r-project.org> on behalf of Roman Hillje via Bioc-devel <bioc-devel using r-project.org>
> Sent: Monday, March 9, 2020 6:48 AM
> To: bioc-devel using r-project.org <bioc-devel using 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 using 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 using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]