Dear All Any help with this would be appreciated. I am normalizing a number of U13A affy chips with justRMA and upon comparison of the pre- and postnormalization histogram curves, I see what seem to be some anomalies in the post-normalization ones. The post-normalization curves that I have seen from other people most often look much smoother than what I get. I attach two graphs for you to inspect if you wish. 4 chips were used only, all of excellent quality check indices (intensity, gene representation, noise etc). > library(affy) > eset <- ReadAffy() # read in 4 affy U133a chips > hist(eset) # see pre-RMA plot attached > rma_eset <- justRMA() > plotDensity(exprs(rma_eset),col=?red?,xlab=?log intensity?) # see post-RMA plot attached I see the same phenomenon when I work with all 69 of my chips. Ive also tried justRMA-ing the entire set in small 5-chip batches to see if one or more chips in particular may be responsible, but it seems to be a rather widespread issue. Thank you for you kind attention. Lawrence ______________________________ Lawrence Paul Petalidis Ph.D. Candidate University of Cambridge Department of Pathology ______________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: pre rma hist.jpeg Type: image/jpeg Size: 68792 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20031215/d568caf0/prermahist-0001.jpeg -------------- next part -------------- A non-text attachment was scrubbed... Name: post RMA hist.jpeg Type: image/jpeg Size: 68352 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20031215/d568caf0/postRMAhist-0001.jpeg -------------- next part -------------- _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

i dont see any problems with those plots. if you are worried about the unsmoothness around the mode its probably due the smoothing criteria used in the density estimator not being large enough for your data. look at the code for plotDensity or simply use for(i in 1:ncol(exprs(rma_eset))) hist(exprs(rma_eset)[,i],nclass=25) to see that there is really no problem. make nclass big enough and the histograms start getting rough. thats true for any continuos data. On Mon, 15 Dec 2003, Lawrence Paul Petalidis wrote: > > Dear All > Any help with this would be appreciated. I am normalizing a number of U13A > affy chips with justRMA and upon comparison of the pre- and > postnormalization histogram curves, I see what seem to be some anomalies in > the post-normalization ones. The post-normalization curves that I have seen > from other people most often look much smoother than what I get. I attach > two graphs for you to inspect if you wish. 4 chips were used only, all of > excellent quality check indices (intensity, gene representation, noise etc). > > > library(affy) > > eset <- ReadAffy() # read in 4 affy U133a chips > > hist(eset) # see pre-RMA plot attached > > rma_eset <- justRMA() > > plotDensity(exprs(rma_eset),col=?red?,xlab=?log intensity?) # see post-RMA > plot attached > > > I see the same phenomenon when I work with all 69 of my chips. Ive also > tried justRMA-ing the entire set in small 5-chip batches to see if one or > more chips in particular may be responsible, but it seems to be a rather > widespread issue. > > Thank you for you kind attention. > Lawrence > > > ______________________________ > Lawrence Paul Petalidis > Ph.D. Candidate > > University of Cambridge > Department of Pathology > ______________________________ > >