----- Forwarded Message ----- From: "Ina Hoeschele" <inah@vbi.vt.edu> To: bioconductor at stat.math.ethz.ch Sent: Monday, May 24, 2010 5:07:54 PM Subject: microarray data without replication Hi, is there an R package (or some other software) for analyzing microarray data without replication? I have written my own code (essentially based on ASE and data permutation) but am still wondering whether some other software exists that I could try (I'm finding a few genes but not too much). Thanks, Ina

Hi Ina You've not said what microarrays you are using or what type(s) of analysis you want to do. If you're wanting to look for differentially expressed genes from Affymetrix arrays, both bgx and puma can make use of technical error from single arrays per condition. The bgx folks wrote a paper about doing this: http://www.biomedcentral.com/1471-2105/7/353/abstract/ Of course, this is no substitute for using biological replicates... Best wishes Richard Ina Hoeschele wrote: > > ----- Forwarded Message ----- > From: "Ina Hoeschele" <inah at="" vbi.vt.edu=""> > To: bioconductor at stat.math.ethz.ch > Sent: Monday, May 24, 2010 5:07:54 PM > Subject: microarray data without replication > > Hi, > is there an R package (or some other software) for analyzing microarray > data without replication? I have written my own code (essentially based > on ASE and data permutation) but am still wondering whether some other > software exists that I could try (I'm finding a few genes but not too > much). Thanks, Ina > > _______________________________________________ > 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 > -- Dr Richard D Pearson richard.pearson at well.ox.ac.uk Wellcome Trust Centre for Human Genetics http://www.well.ox.ac.uk/~rpearson University of Oxford Tel: +44 (0)1865 617890 Roosevelt Drive Mob: +44 (0)7971 221181 Oxford OX3 7BN, UK Fax: +44 (0)1865 287664