Thanks for the quick and exhaustive reply!! Regarding the missing heatmap - the files were indeed missing (this was on a g5 mac with 3 gigs of ram; R 2.7.2 with arrayQualityMetrics_1.6.1). But when I reran arrayQualityMetrics on a linux machine with 64 gigs of ram the heatmap files were generated (this time under a freshly compiled R2.8 RC 2008-10-14 with arrayQualityMetrics_1.7.17). Best, Yannick On Oct 16, 2008, at 12:08 , Audrey Kauffmann wrote: > Hi Yannick, > > - Here is how the outlier detection is performed: > For the MA-plot, the mean of the absolute value of M is computed > for each array and those that lie beyond the extremes of the > boxplot's whiskers are considered as possible outliers arrays. The > same approach, i.e. using the whiskers of the boxplot, is applied > to the following: the mean and interquartile range (IQR) from the > boxplots and NUSE, the sums of the rows of the distance matrix (for > the heatmap), and the amplitude of low frequencies of the > periodogram (for the spatial intensity distribution). In the case > of the RLE plot, any array with a median RLE higher than 0.1 is > considered as a possible outlier. > To decide whether or not you should remove some chips from your > analysis, I advice you to run the report after normalisation. If > after normalisation, some arrays are flagged with a star in several > quality assessment sections, I would remove it. Of course, it > mainly depends on the context. For instance, if there is a > biological good reason for an array to be an outlier, keep it. > > - To see the "inside" of the arrayQualityMetrics function: > showMethods("arrayQualityMetrics") > gives you the classes for which a method exists. Then you can see > the function for one of this class using selectMethod, for instance: > > selectMethod("arrayQualityMetrics","AffyBatch") > > However, if you are willing to modify it, you can download the > source of the package, the functions are in the directory > "arrayQualityMetrics/R". > I am currently working on a new version of the package where it > will be easier to adapt the functions and to modify the report. If > you are interested, you can have a look at the devel branch of > Bioconductor, I will update the development version of the package > soon. > > - For the missing heatmap, I have sometimes seen that the plot is > done but for some reason does not show in the report. You can check > the files heatmap.png and heamapt.pdf in the directory where you > created the report. > > Audrey > > > Yannick Wurm wrote: >> Morning List, >> >> I've been toying with arrayQualityMetrics which gives me a great >> overview of my data without too much work. >> >> Several things are still unclear to me though: >> >> - how does it calculate the '*' that indicate that a chip may >> be bad. How stringent/conservative are they? Because several of my >> spotted cDNA chips show up as having issues, and now I'm unsure >> whether or not I should remove them from my analysis. >> >> - is there any way to "see inside" the package? I'd like to >> see how the stringency is calculated, and adapt some of the output >> formatting. But when I try to look inside, all I get is something >> called "environment": >> > arrayQualityMetrics >> >> standardGeneric for "arrayQualityMetrics" defined from >> package "arrayQualityMetrics" >> function (expressionset, outdir = getwd(), force = FALSE, >> do.logtransform = FALSE, >> split.plots = FALSE, intgroup = "Covariate") >> standardGeneric("arrayQualityMetrics") >> <environment: 0x4882ad8=""> >> Methods may be defined for arguments: expressionset, >> outdir, force, do.logtransform, split.plots, intgroup >> Use showMethods("arrayQualityMetrics") for currently >> available ones. >> - on one NChannelSet containing 280 slides, >> arrayQualityMetrics didn't calculate the heatmap. But didn't >> display any error messages either. Possibly because of memory >> contraints on my 3GB mac? >> >> Thanks for putting me on the track to resolving this. >> >> Best, >> >> Yannick >> >> -------------------------------------------- >> yannick . wurm @ unil . ch >> Ant Genomics, Ecology & Evolution @ Lausanne >> http://www.unil.ch/dee/page28685_fr.html >> >> _______________________________________________ >> 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 > http://www.ebi.ac.uk/~audrey >