Hi Assa are you using the updated version of 'arrayQualityMetrics'? (see: https://stat.ethz.ch/pipermail/bioconductor/2010-November/036459.html ) What is for you the result of nrow(rawData) ? (The function assumes that 'nrow' and 'ncol' applied to the data object provide the correct spatial coordinates) I suspect that the spatial plot (sub)function does not work for some array types. However, you should get a report containing all the other types of report sections. And I hope the spatial plots can be fixed for the next release. Best wishes Wolfgang Il Nov/16/10 8:37 AM, Assa Yeroslaviz ha scritto: > Hi Jim, Bioconductor users > > thanks for the note. I tried the package and it looks good. > > Unfortunately i get some error messages when analysinf the raw data. > >> rawData<- ReadAffy(widget=T) # creating the affybatch from CEL files. >> >> arrayQualityMetrics(rawData, "data_raw", force= TRUE, do.logtransform= TRUE) # QC of raw data > The directory 'data_raw' has been created. > Error in seq_len(maxr) : > argument must be coercible to non-negative integer > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > (loaded the KernSmooth namespace) > [[1]] > > [[2]] > > Warning message: > In arrayQualityMetrics(rawData, "data_raw", force = TRUE, > do.logtransform = TRUE) : > Could not draw spatial distribution of intensities > > Error in sfs(x) : > error in evaluating the argument 'object' in selecting a method for > function 'sfs' > > But after normalizing the datausing the gcRMA algorithm I don't get > these errors. > >> normData<- gcrma(rawData) # GC-RMA normalization > Adjusting for optical effect............Done. > Computing affinitiesLoading required package: AnnotationDbi > .Done. > Adjusting for non-specific binding............Done. > Normalizing > Calculating Expression > Warning message: > closing unused connection 3 (QMreport.html) >> arrayQualityMetrics(normData, "data_norm", force= TRUE, do.logtransform= TRUE) # QC of normalized data (after RMA) > The directory 'data_norm' has been created. > [[1]] > > [[2]] > >> > > > Does anyone has an idea as to what these errors means? > I read in the mailing lists, that the spatial dist. is quite a memory > consuming procedure, but I am using a 64Bit Unix server (Ubuntu) with > 48GB RAM. So I don't think that can be a problem. > Beside I don't understand the other errors. > > I do get as a result a list of images as I suppose. I just want to > make sure, that these error messages have nothing to do with the > results themselves. > > I hope someone can explain them in short. > > Thanks > > Assa > > On Mon, Nov 15, 2010 at 15:12, James W. MacDonald<jmacdon at="" med.umich.edu=""> wrote: >> Hi Assa, >> >> You might try the arrayQualityMetrics package. >> >> Best, >> >> Jim >> >> >> >> On 11/15/2010 4:59 AM, Assa Yeroslaviz wrote: >>> >>> Hi everybody, >>> >>> I have a set of drosophile genome 2.0 arrays to analyze. I wanted to >>> start with a quality control using the affyQCReport package. >>> >>> according to the manual I set the enivironment. >>>> >>>> setQCEnvironment("drosgenome2cdf", >>>> "/home/AYeroslaviz/R/x86_64-pc-linux-gnu- library/2.12/simpleaffy/extdata") >>> >>> and run the QCreport on the raw data >>>> >>>> QCReport(rawData) >>> >>> unfortunately I get an error message >>> >>> Error: NAs in foreign function call (arg 5) >>> >>> Can someone please tell me what the meaning of this error. I tried to >>> search the mailing lists but didn't find anything. >>> If AffyQCReport doesn't work, do I have an alternative? >>> >>> Thanks >>> >>> Assa >>> >>>> sessionInfo() >>> >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] tools tcltk splines stats graphics grDevices utils >>> [8] datasets methods base >>> >>> other attached packages: >>> [1] simpleaffy_2.26.0 genefilter_1.32.0 >>> [3] drosophila2cdf_2.7.0 arrayQualityMetrics_3.2.1 >>> [5] vsn_3.18.0 affyPLM_1.26.0 >>> [7] gcrma_2.22.0 tkWidgets_1.28.0 >>> [9] widgetTools_1.28.0 siggenes_1.24.0 >>> [11] multtest_2.6.0 samr_1.28 >>> [13] impute_1.24.0 MASS_7.3-5 >>> [15] vioplot_0.2 sm_2.2-4.1 >>> [17] preprocessCore_1.10.0 DynDoc_1.28.0 >>> [19] cluster_1.13.1 affydata_1.11.10 >>> [21] affycomp_1.26.0 affyQCReport_1.28.0 >>> [23] lattice_0.19-13 affy_1.28.0 >>> [25] Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 annotate_1.28.0 AnnotationDbi_1.12.0 >>> [4] beadarray_2.0.2 Biostrings_2.18.0 DBI_0.2-5 >>> [7] grid_2.12.0 hwriter_1.2 IRanges_1.8.2 >>> [10] latticeExtra_0.6-14 limma_3.6.6 marray_1.28.0 >>> [13] RColorBrewer_1.0-2 RSQLite_0.9-1 stats4_2.12.0 >>> [16] survival_2.35-8 SVGAnnotation_0.7-2 XML_2.6-0 >>> [19] xtable_1.5-6 >>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > > _______________________________________________ > 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