Dear John, I wrote the warning in the ?lmscFit documentation about it being somewhat experimental more than two and a half years ago, when the function were first introduced into the limma package. I've done much more testing since then, and the function has stood the test of time, so I'll remove the warning. Best wishes Gordon >[BioC] limma help - choosing an approach >john seers (IFR) john.seers at bbsrc.ac.uk >Thu Sep 14 12:19:39 CEST 2006 > >Hello Naomi (and anyone else) > >Thanks again for your help. It has been extremely helpful. Almost there >I think, though I am still just doing it on autopilot and not quite sure >how meaningful this is. I am slightly worried by the limma documentation >which describes the single channel analysis as "experimental" so >combined with my lack of understanding makes me feel quite uncertain. >Anyway I can run it now and pull out lists of genes - though what they >mean I am not sure yet. >...

Dear Gordon and rest, I've been following the outcome of this thread carefully and am persuing a single-channel analysis for a couple of Agilent arrays as well. Do you (or anyone else for that matter) happen to know if there are any publications available that implemented or have tested this approach? Best wishes, Stan PhD Student Dept. of Human Biology & BiGCaT Bioinformatics PO BOX 616 UNS 40 Room 5.578 6200 MD Maastricht Tel: +31 (0) 433882913 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon Smyth Sent: 15 September 2006 06:09 To: BioC Mailing List Subject: [BioC] limma help - choosing an approach Dear John, I wrote the warning in the ?lmscFit documentation about it being somewhat experimental more than two and a half years ago, when the function were first introduced into the limma package. I've done much more testing since then, and the function has stood the test of time, so I'll remove the warning. Best wishes Gordon >[BioC] limma help - choosing an approach >john seers (IFR) john.seers at bbsrc.ac.uk >Thu Sep 14 12:19:39 CEST 2006 > >Hello Naomi (and anyone else) > >Thanks again for your help. It has been extremely helpful. Almost there >I think, though I am still just doing it on autopilot and not quite sure >how meaningful this is. I am slightly worried by the limma documentation >which describes the single channel analysis as "experimental" so >combined with my lack of understanding makes me feel quite uncertain. >Anyway I can run it now and pull out lists of genes - though what they >mean I am not sure yet. >... _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor