Dear Audrey, thanks for your reply. I tried re-installing the package from bioc. It gave the same results. I later installed 2.5 version of the software. This also gave the same plots. There is still the same problem with ordering of colors. I see you asked me to use version 2.4.1 but I could not find it in the release or development version. Am I looking at the wrong places? Please let me know and thanks for your time... Thank you Lohith P.S: I know this might be just a simple bug in the program and I wanted to see if I can successfully tweak the R script for the software but I did not find the R script in both the release and development versions..It would be great to see the code.. On Thu, Oct 29, 2009 at 2:41 AM, Audrey Kauffmann wrote: > Dear Jeremy, > > Thank you for reporting this. You were right there was a problem in the > code for the ordering of the colours. > I have now corrected it, so arrayQualityMetrics version 2.4.1 should be > working fine. > Please let me know if you keep experiencing problems. > > Best wishes, > Audrey > > jeremy wilson wrote: > >> Dear BioConductors, >> >> I am using arrayQualityMetrics software package to do the QA. I very much >> like all the QA plots it produces including the latest PCA plot in one >> report. I am using the latest version of R(2.10) and BioC (2.5). I am >> facing >> a problem with inappropriate labeling of covariates. Please see the >> attached >> plots. >> I have total of 69 samples. I asked the software to label the plots based >> on >> a covariate, the summary of which is as below: >> >> Notation total number of samples in order >> V 23 >> G 38 >> N 8 >> >> The problem is that it does not label the graphs correctly in the plots!! >> In >> the plots, the first set of samples correspond to V, the next 38 samples >> for >> G and the last 8 for N. In the boxplot for example, the G was labelled RED >> and this should correspond to 38 samples but in the plot, the boxplots >> corresponding to these 38 samples were colored GREEN. The ones that were >> labeled RED correspond to 8 'N' samples which should be represented in >> blue >> according to the label at the top of plot. Likewise for the other two. I >> think it can be better understood at the first glance of the plots. >> >> The phenotype of the samples was given correctly. >> Following is the code I used for generating the aqm report. >> >> library(arrayQualityMetrics) >> arrayQualityMetrics(rat.ab, do.logtransform=TRUE, outdir="QA", >> intgroup="Material", grouprep=TRUE) >> >> I have attached only a few plots. I can produce all of them if it helps... >> It might take some time for the post to reach the mailing list as the >> earlier one I posted with a few more plots was held for moderator's >> approval >> as the size of the message body is over the limit! >> >> Please let me know what is wrong. >> Thanks in advance! >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Audrey Kauffmann > EMBL - EBI > Cambridge UK > +44 (0) 1223 492 631 http://www.ebi.ac.uk/~audrey > > [[alternative HTML version deleted]]