Dear R and edgeR community, Good day. I have a question about parsing values from table. I have an R object, *ps*which contained a set of tags let's say "AS123645", "AF239456", "AG324567" and so on. I would like to parse the reading which match to tags in the *ps* from a * DGEExact$table*. The DGEExact$table is generated with *edgeR* when performed the *exactTest* for the RNA-Seq data. The *DGEExact$table* is looks like: An object of class "DGEExact" $table logFC logCPM PValue AA556146 0.3700360 0.6844266 0.86258137 AA556148 -0.6134484 3.7174273 0.09524158 AA556155 0.3467066 1.7382440 0.63816061 58029 more rows ... Could someone kindly please advice me? Thank you very much. Best regards, KJ Lim [[alternative HTML version deleted]]

Hi KJ Lim, On 8/21/2012 9:43 AM, KJ Lim wrote: > Dear R and edgeR community, > > Good day. > > I have a question about parsing values from table. I have an R object, > *ps*which contained a set of tags let's say "AS123645", "AF239456", > "AG324567" > and so on. If you are having questions about simple things like subsetting matrices, I would highly recommend reading 'An Introduction to R', which comes with R. You can get to it by typing help.start() at an R prompt, and then choosing the 'Manuals' link. You won't get very far without knowing how to do simple manipulations like this. For now, please note that you can subset matrices in numerous ways, one of which is by passing a character vector of the row names: subtable <- DGEExact$table[c("AS123645","AF239456", "AG324567"),] Best, Jim > > I would like to parse the reading which match to tags in the *ps* from a * > DGEExact$table*. The DGEExact$table is generated with *edgeR* when > performed the *exactTest* for the RNA-Seq data. > > The *DGEExact$table* is looks like: > > An object of class "DGEExact" > $table > logFC logCPM PValue > AA556146 0.3700360 0.6844266 0.86258137 > AA556148 -0.6134484 3.7174273 0.09524158 > AA556155 0.3467066 1.7382440 0.63816061 > 58029 more rows ... > > > Could someone kindly please advice me? > > Thank you very much. > > Best regards, > KJ Lim > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099