Hi Ryan, Thanks for your message and I will look into this.
Jack ---- Yuelin Jack Zhu Biologist (Bioinformatics) Genetics Branch/CCR/NCI/NIH Tel: (301)496-4527 FAX: (301) 402-3241 E-mail: zhuj...@mail.nih.gov On Thu, Nov 17, 2016 at 5:20 PM, Ryan C. Thompson <r...@thompsonclan.org> wrote: > Hello, > > I was recently bitten by an unexpected behavior in the sraConvert function > from the SRAdb package. I wanted to fetch the other SRA IDs associated with > the SRX numbers of 32 samples, and I used the sraConvert function to do so. > However, I did not realized that sraConvert returns the results in > arbitrary order rather than sorting them in the same order as the input, so > I just used cbind to add these IDs to my existing sample table. This > effectively shuffled my samples, and I did not notice until far downstream > when I started making PCA plots and the clustering made no sense. > > I leave it up to the developers of the SRAdb package to decide whether or > not this is a bug, but I think it should at least be documented that the > sort order of the output of sraConvert is arbitrary and will not > necessarily match the input. > > -Ryan > > _______________________________________________ > 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