Dear Bioconductors, I try to use marrayQualityPlots from the arrayQuality package on a raw data object generated by limma. I get an error message that I do not understand (see below). My installation is the following: Mac OS 10.2.8 Darwin 6.8 R 2.0.1 arrayQuality 1.0.7 hexbin 1.0.10 Any hint would be highly appreciated. Thanks! Georg here is the error message: > maQualityPlots(RG, DEBUG=TRUE) [1] "function starting" [1] 15552 12 [1] "Re-evaluate Weight" check Control color code 2 3 4 5 6 [1] "Set up data and normalization" [1] "Reading normalization parameters" list() Using normalization method: p [1] "Name the output file" [1] "hps-d4-mwg-p4-slide26-10" [1] "Name of output device" [1] "diagPlot.hps-d4-mwg-p4-slide26-10.png" [1] "start layout" [1] "start 1" [1] "start 2" Error in seq.default(0, 1, length = min(17, maxcnt)) : Length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf

Dear Georg, It looks like maQualityPlots is crashing in one the internal functions plotting the density of your data, but I never saw this error before. Could send me the original image processing file and the command you used to generate your RGList (or your RG object if you don't have the file) so that I can find what is causing this problem? Thank you very much for your help, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg Otto Sent: Wednesday, February 09, 2005 12:45 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] problem using arrayQuality package Dear Bioconductors, I try to use marrayQualityPlots from the arrayQuality package on a raw data object generated by limma. I get an error message that I do not understand (see below). My installation is the following: Mac OS 10.2.8 Darwin 6.8 R 2.0.1 arrayQuality 1.0.7 hexbin 1.0.10 Any hint would be highly appreciated. Thanks! Georg here is the error message: > maQualityPlots(RG, DEBUG=TRUE) [1] "function starting" [1] 15552 12 [1] "Re-evaluate Weight" check Control color code 2 3 4 5 6 [1] "Set up data and normalization" [1] "Reading normalization parameters" list() Using normalization method: p [1] "Name the output file" [1] "hps-d4-mwg-p4-slide26-10" [1] "Name of output device" [1] "diagPlot.hps-d4-mwg-p4-slide26-10.png" [1] "start layout" [1] "start 1" [1] "start 2" Error in seq.default(0, 1, length = min(17, maxcnt)) : Length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Georg, If maQualityPlots is too slow, you can try to speed up the process by changing the default normalization method to global median or loess. To do so, you can try: maQualityPlots(RG, norm="m") The diagnostic plot from arrayQuality is pretty complex to generate, and unfortunately making the font bigger requires a lot of modifications. The resulting plot should be of size 1600x1200. You should also be able to zoom in the png image using any image viewer until the plots and the characters are big enough. If not, could you please send me your file so that I can investigate what causes this problem? I will try to fix the postscript extension problem as soon as possible. Regards, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg Otto Sent: Thursday, February 10, 2005 12:22 PM To: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] problem using arrayQuality package Dear Agnes, thanks for your offer to help. It might have been a problem with memory, since today i tried it with data from only two hybridisations (instead of twelve) and it worked, although it took a long computation time. I will let you know when I found out more. Now i have a different problem: I do not know how to do with the png file of the diagnostic plots (in fact, I do not know much about graphics at all). The plots and the characters are too small to be readable and magnifying does not help. Unfortunately, postscript does not work as an output file, it gives me the error message: > maQualityPlots(RG, DEBUG=TRUE, dev="postscript") [1] "function starting" [1] 17328 2 [1] "Re-evaluate Weight" check Control color code 2 3 4 5 [1] "Set up data and normalization" [1] "Reading normalization parameters" list() Using normalization method: p [1] "Name the output file" [1] "hps-d4-cg-p4-slide16-25" [1] "Name of output device" [1] "diagPlot.hps-d4-cg-p4-slide16-25.ps" [1] "start layout" Error in ifelse(onefile, "Rplots.ps", "Rplot%03d.ps") : Object "onefile" not found Now my question is: what is wrong with postscript here? Or alternatively, is there a way to produce larger png files with larger, readable characters and plots? Thanks a lot, Georg On Thursday, February 10, 2005, at 03:21 AM, Paquet, Agnes wrote: > Dear Georg, > > It looks like maQualityPlots is crashing in one the internal functions > plotting the density of your data, but I never saw this error before. > > Could send me the original image processing file and the command you > used to generate your RGList (or your RG object if you don't have the > file) so that I can find what is causing this problem? > > Thank you very much for your help, > > Agnes > >> -----Original Message----- >> From: bioconductor-bounces@stat.math.ethz.ch >> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg >> Otto >> Sent: Wednesday, February 09, 2005 12:45 PM >> To: bioconductor@stat.math.ethz.ch >> Subject: [BioC] problem using arrayQuality package >> >> Dear Bioconductors, >> >> I try to use marrayQualityPlots from the arrayQuality package on a raw >> data object generated by limma. I get an error message that I do not >> understand (see below). >> >> My installation is the following: >> >> Mac OS 10.2.8 >> Darwin 6.8 >> R 2.0.1 >> arrayQuality 1.0.7 >> hexbin 1.0.10 >> >> Any hint would be highly appreciated. Thanks! >> >> Georg >> >> here is the error message: >> >> maQualityPlots(RG, DEBUG=TRUE) >> [1] "function starting" >> [1] 15552 12 >> [1] "Re-evaluate Weight" >> check Control color code 2 3 4 5 6 >> [1] "Set up data and normalization" >> [1] "Reading normalization parameters" >> list() >> Using normalization method: p >> [1] "Name the output file" >> [1] "hps-d4-mwg-p4-slide26-10" >> [1] "Name of output device" >> [1] "diagPlot.hps-d4-mwg-p4-slide26-10.png" >> [1] "start layout" >> [1] "start 1" >> [1] "start 2" >> Error in seq.default(0, 1, length = min(17, maxcnt)) : >> Length must be non-negative number >> In addition: Warning message: >> no finite arguments to max; returning -Inf >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> -- Georg Wilhelm Otto Max-Planck-Institute for Developmental Biology Spemannstrasse 35/III D-72076 Tuebingen Germany phone: +49-7071-601 301 http://www.eb.tuebingen.mpg.de _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor