Hi Folks, I have read an article on two color microarray hybridization. The authors have pooled control samples (1), this mixture was lablled, hybridized together with separately labelled treated (x) samples on x microarrays ( Treated samples were not pooled). Do you think that is good idea? Narendra Imperial College of Medicine, London W2 1PG UK [[alternative HTML version deleted]]

This is (quite) common practice. The pooled sample represents a common reference for the treated samples. A common reference experimental design *can* have certain advantages over direct comparisons, such as easy extensibility and ease of interpretation. Pooling the control samples simply ensures that the common reference is more generic (hopefully) and lights up more spots (hopefully). Mick -----Original Message----- From: Kaushik, Narendra K [mailto:n.kaushik@imperial.ac.uk] Sent: 16 September 2004 22:56 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Is it right? Hi Folks, I have read an article on two color microarray hybridization. The authors have pooled control samples (1), this mixture was lablled, hybridized together with separately labelled treated (x) samples on x microarrays ( Treated samples were not pooled). Do you think that is good idea? Narendra Imperial College of Medicine, London W2 1PG UK [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

it depends on whether the contol is of interest. if the objective of this study is to compare the differences between control and treated samples, then the design described below is not appropriate. However, it is OK if the researcher is not interested in the control sample at all. Caimiao ----- Original Message ----- From: "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> To: "Kaushik, Narendra K" <n.kaushik@imperial.ac.uk>; <bioconductor@stat.math.ethz.ch> Sent: Friday, September 17, 2004 1:07 AM Subject: RE: [BioC] Is it right? > This is (quite) common practice. The pooled sample represents a common > reference for the treated samples. A common reference experimental > design *can* have certain advantages over direct comparisons, such as > easy extensibility and ease of interpretation. Pooling the control > samples simply ensures that the common reference is more generic > (hopefully) and lights up more spots (hopefully). > > Mick > > -----Original Message----- > From: Kaushik, Narendra K [mailto:n.kaushik@imperial.ac.uk] > Sent: 16 September 2004 22:56 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Is it right? > > > Hi Folks, > > I have read an article on two color microarray hybridization. The > authors have pooled control samples (1), this mixture was lablled, > hybridized together with separately labelled treated (x) samples on x > microarrays ( Treated samples were not pooled). Do you think that is > good idea? > > Narendra > Imperial College of Medicine, > London W2 1PG > UK > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >