Hi, I would like to use limma to analyse affymetrix data, but my affy data is not an eset object because I have done the low-level analysis in a different software program. How can I attach probe IDs to the toptable results when the initial affy data is not an eset object. regards Anthony -- ______________________________________________ Anthony Bosco - PhD Student Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au

Anthony Bosco wrote: > Hi, > > I would like to use limma to analyse affymetrix data, but my affy data > is not an eset object because I have done the low-level analysis in a > different software program. > > How can I attach probe IDs to the toptable results when the initial affy > data is not an eset object. You can always use the genelist argument of topTable to specify the names of your genes. See ?topTable. Jim > > > regards > > > Anthony -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

As Dr. MacDonald pointed out, you can use the genelist argument in topTable. I had a similar problem and Gordon Smyth said that this feauture would be available in the next release. https://stat.ethz.ch/pipermail/bioconductor/2005-February/007832.html Regards, Adai On Mon, 2005-03-14 at 07:40 +0100, Anthony Bosco wrote: > Hi, > > I would like to use limma to analyse affymetrix data, but my affy > data is not an eset object because I have done the low-level analysis > in a different software program. > > How can I attach probe IDs to the toptable results when the initial > affy data is not an eset object. > > > regards > > > Anthony