Re: [R] Check a list of genes for a specific GO term

2013-07-08 Thread Martin Morgan
Please ask follow-up questions about Bioconductor packages on the Bioconductor mailing list. http://bioconductor.org/help/mailing-list/mailform/ If you are interested in organisms rather than chips, use the organism package, e.g., for Homo sapiens library(org.Hs.eg.db) df0 = select(org.H

Re: [R] Check a list of genes for a specific GO term

2013-07-07 Thread Chirag Gupta
Hi I think I asked the wrong question. Apologies. Actually I want all the GO BP annotations for my organism and from them I want to retain only those annotations which annotate less than a specified number of genes. (say <1000 genes) I hope I have put it clearly. sorry again. Thanks! On Sun,

Re: [R] Check a list of genes for a specific GO term

2013-07-07 Thread Martin Morgan
In Bioconductor, install the annotation package http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData corresponding to your chip, e.g., source("http://bioconductor.org/biocLite.R";) biocLite("hgu95av2.db") then load it and select the GO terms corresponding to your prob

Re: [R] Check a list of genes for a specific GO term

2013-07-07 Thread Rui Barradas
Hello, Your question is not very clear, maybe if you post a data example. To do so, use ?dput. If your data frame is named 'dat', use the following. dput(head(dat, 50)) # paste the output of this in a post If you want to get the rownames matching a certain pattern, maybe something like the f