Hi, I am using Zebrafish Gene 1.1 ST Array Strip from Affymetrix. Affymetrix categorizes the transcript clusters as: main - part of the main design control->affx - a standard AFFX control control->chip - a chip control control->bgp->antigenomic - contains antigenomic background probes control->bgp->genomic - contains genomic background probes normgene->exon - from an exonic region of a normalization control gene normgene->intron - from an intronic region of a normalization control gene rescue - contains probes tiled across an mRNA transcript which either did not align to the genome, or aligned poorly I was wondering if it makes sense to use the "rescue" transcript clusters when searching for differentially expressed genes. Sorry that this question is not directly related to bioconductor, but I am not sure where to ask for this (I tried Affymetrix las month, but still haven't got an answer) Best, Joao Lopes Instituto Gulbenkian de Ciencia

Hi Joao, How about I reverse the question. Does it make sense to you to use data generated using probes that align poorly at best to the genome of the species you are working with? If so, why? Best, Jim On Tuesday, September 17, 2013 1:59:52 PM, Joao Sollari Lopes wrote: > Hi, > > I am using Zebrafish Gene 1.1 ST Array Strip from Affymetrix. > Affymetrix categorizes the transcript clusters as: > > main - part of the main design > control->affx - a standard AFFX control > control->chip - a chip control > control->bgp->antigenomic - contains antigenomic background probes > control->bgp->genomic - contains genomic background probes > normgene->exon - from an exonic region of a normalization control gene > normgene->intron - from an intronic region of a normalization control > gene > rescue - contains probes tiled across an mRNA transcript which either > did not align to the genome, or aligned poorly > > I was wondering if it makes sense to use the "rescue" transcript > clusters when searching for differentially expressed genes. > > Sorry that this question is not directly related to bioconductor, but > I am not sure where to ask for this (I tried Affymetrix las month, but > still haven't got an answer) > > Best, > Joao Lopes > Instituto Gulbenkian de Ciencia > > _______________________________________________ > 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