Lana: You are right. The numbers do seem to be log-ratios. > dat=ReadAffy() > eset=mas5(dat) > myqc=qc(dat) > ratios(myqc) actin3/actin5 actin3/actinM gapdh3/gapdh5 gapdh3/gapdhM ac1.CEL 0.2878089 0.2367158 -0.2767954 -0.1206753 ac2.CEL 0.2736803 0.2636448 -0.3175412 -0.1373552 I want to check the gapdh 3/5 ratio numbers. First, I have to find out which probe sets? > gaps=exprs(eset[grep("Gapdh",featureNames(eset)),]) > gaps ac1.CEL ac2.CEL AFFX-GapdhMur/M32599_3_at 29362.31 43935.84 AFFX-GapdhMur/M32599_5_at 35572.47 54753.06 AFFX-GapdhMur/M32599_M_at 31923.99 48324.46 I calculate the ratio of 3_at against 4_at and log-transform. > log2(gaps[1,]/gaps[2,]) ac1.CEL ac2.CEL -0.2767954 -0.3175412 These numbers match with the output of ratios(myqc) third column. > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] mouse4302cdf_2.3.0 simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 [5] genefilter_1.22.0 survival_2.34-1 affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.3 [4] DBI_0.2-4 preprocessCore_1.4.0 RSQLite_0.7-1 Saroj Lana Schaffer wrote: > Saroj, > Thank you for your pdf reference. > I know what is generally written about these GAPDH ratios, but > the ratios from Simpleaffy have never made sense. > First, these ratios are not the same as the ratios from the Affy > software or from calculated Mas5.0 ratios. > Second, there are not only ratios between 0 and 1, there are also > negative ratios. > Third, the only way this makes sense, is that these are log ratios. > > Lana > > -----Original Message----- > From: Saroj K Mohapatra [mailto:saroj at vt.edu] > Sent: Friday, June 12, 2009 10:03 AM > To: Lana Schaffer > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Simpleaffy QC > > Hi Lana: > > "GAPDH 3':5' values are plotted as circles. According to Affymetrix they > should be about 1. GAPDH values that are considered potential outliers > (ratio > 1.25) are coloured red, otherwise they are blue." -- > http://bioinformatics.picr.man.ac.uk/downloads/QCandSimpleaffy.pdf > > I think the color of the 'circle' symbol matters more than its actual > position; red suggests a ratio > 1.25. The x axis labels refer to scale > factor. > > Best, > > Saroj > > Lana Schaffer wrote: > >> Hi, >> The plot(qc) command prints a plot of the Affy QC metrics. >> The GAPDH ratio is a bit confusing because the ratios range from <0 to >> > > >>> 3. How can the GAPDH ratio be 0? >>> >> Could these values represent log of the ratio? >> >> 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 >> >> _______________________________________________ >> 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 >> >> >> > > >