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Wolfgang, You are correct in assuming that I am refering to the output of a recent devel-version of the affyQAReport function in the affyQCReport package. R 2.5.0 Pre-release library("affyQCReport") library("affydata") library(GeneMeta) celpath <- "C:/.../" CLL <- ReadAffy(celfile.path=celpath,widget=F) rep2 = affyQAReport(CLL) openQAReport(rep2) Thank you for your helpful information. Lana ----- Original Message ----- From: "Wolfgang Huber" <huber@ebi.ac.uk> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Thursday, January 18, 2007 11:59 AM Subject: Re: [BioC] Quality Assessment > Dear Lana, > >> I am trying to understand the diagnostic plot of the MAD pairwise >> differences of the M-values and how this plot can detect outliers. >> I looked at the example for the CLL data and did not detect any >> differences, but would like to know how to detect any differences. >> All the small boxes are different colors but are mirrored pairwise >> intensities. The notes say: "Arrays whose distance matrix entries >> are way different give cause for suspicion". However, the color >> intensities look different?? Please explain how to know if they >> are "way different". > > Hmm, which package and function are you refering to and which version? > > The following assumes that you refer to the output of a recent > devel-version of the affyQAReport function in the affyQCReport package? > > The matrix is symmetric because the MAD distance is. More details are > given in the man page of "dist2". This is an exploratory plot that can > help detecting (a) outlier arrays and (b) batch effects. There are no > objective numeric thresholds when to call something an outlier, it > depends on your context, that's why the text is vague. > > If there are outliers, you will expect to see vertical and horizontal > stripes in the plot of darker color. Batch effects that are aligned to > the order of the arrays as they are read in can be seen as blocks along > the diagonal. If you see neither, you are lucky, and the data passes > this quality criterion! > > I have added some more text to explain this to the report template. > > Hope this helps > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > PS Please do remember to state the output of sessionInfo() and the > relevant R code for reproducing the subject of your question. > > >> >> Lana Schaffer >> Biostatistics/Informatics >> The Scripps Research Institute >> DNA Array Core Facility >> La Jolla, CA 92037 >> (858) 784-2263 >> (858) 784-2994 >> schaffer at scripps.edu >> >

Dear Lana, > I am trying to understand the diagnostic plot of the MAD pairwise > differences of the M-values and how this plot can detect outliers. > I looked at the example for the CLL data and did not detect any > differences, but would like to know how to detect any differences. > All the small boxes are different colors but are mirrored pairwise > intensities. The notes say: "Arrays whose distance matrix entries > are way different give cause for suspicion". However, the color > intensities look different?? Please explain how to know if they > are "way different". Hmm, which package and function are you refering to and which version? The following assumes that you refer to the output of a recent devel-version of the affyQAReport function in the affyQCReport package? The matrix is symmetric because the MAD distance is. More details are given in the man page of "dist2". This is an exploratory plot that can help detecting (a) outlier arrays and (b) batch effects. There are no objective numeric thresholds when to call something an outlier, it depends on your context, that's why the text is vague. If there are outliers, you will expect to see vertical and horizontal stripes in the plot of darker color. Batch effects that are aligned to the order of the arrays as they are read in can be seen as blocks along the diagonal. If you see neither, you are lucky, and the data passes this quality criterion! I have added some more text to explain this to the report template. Hope this helps Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber PS Please do remember to state the output of sessionInfo() and the relevant R code for reproducing the subject of your question. > > Lana Schaffer > Biostatistics/Informatics > The Scripps Research Institute > DNA Array Core Facility > La Jolla, CA 92037 > (858) 784-2263 > (858) 784-2994 > schaffer at scripps.edu >