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Question: ArrayQualityMetrics: Problem with labels in plots. A bug??
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gravatar for jeremy wilson
8.0 years ago by
jeremy wilson150
jeremy wilson150 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! -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot.png Type: image/png Size: 11278 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20091028="" ed0e539f="" attachment.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: density.png Type: image/png Size: 5232 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20091028="" ed0e539f="" attachment-0001.png="">
ADD COMMENTlink modified 8.0 years ago by audrey280 • written 8.0 years ago by jeremy wilson150
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gravatar for audrey
8.0 years ago by
audrey280
audrey280 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 at 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
ADD COMMENTlink written 8.0 years ago by audrey280
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 <audrey@ebi.ac.uk> 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]]
ADD REPLYlink written 8.0 years ago by jeremy wilson150
Dear Jeremy, Sorry I did not think about this, I think it takes a couple of days between the moment the developer modifies the version of the package and the moment you can actually install it using biocLite. You should be able to install version 2.4.1 after the week-end. Best wishes, Audrey jeremy wilson wrote: > 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 <audrey at="" ebi.ac.uk=""> <mailto:audrey at="" ebi.ac.uk="">> 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 at stat.math.ethz.ch > <mailto: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 > > > -- > Audrey Kauffmann > EMBL - EBI > Cambridge UK > +44 (0) 1223 492 631 http://www.ebi.ac.uk/~audrey > <http: www.ebi.ac.uk="" %7eaudrey=""> > > -- Audrey Kauffmann EMBL - EBI Cambridge UK +44 (0) 1223 492 631 http://www.ebi.ac.uk/~audrey
ADD REPLYlink written 8.0 years ago by audrey280
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