Hi Jim, Thanks for your answer, it's my first experience with Affy data, I used to work with Agilent before. I take a look at the vignette and generated the requested file based on the info about the htmg430pm data : array htmg430pmcdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_5_at ratio actin3/actinM AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_M_at ratio gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX- GapdhMur/M32599_5_at ratio gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX- GapdhMur/M32599_M_at report works well for normalized data, but for raw data i get the following errors: The report will be written in directory 'report'. Error : NAs in foreign function call (arg 1) Error in density.default(as.matrix(log2(mm(expressionset))), ...) : 'x' contains missing values In addition: Warning message: In aqm.qcstats(expressionset) : 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. Error in obj[[i]]$legend : $ operator is invalid for atomic vectors In addition: Warning message: In arrayQualityMetrics(aBatch, outdir = "report") : Cannot draw the Perfect Match versus MisMatch plot here's the code i'm using : # Identify CEL files. fls <- list.files("/", ".*CEL") # Input raw data aBatch <- ReadAffy(filenames = fls) # Process CEL files using RMA (robust multi-array average). eset <- justRMA(filenames = fls) arrayQualityMetrics(aBatch,outdir = "report_raw") arrayQualityMetrics(eset,outdir = "report_normalized") Any idea about what is wrong with the QC report on raw data ? Thanks in advance. Regards, Ramzi Best, Ramzi ---------------------------------------------------------------- On Mon, Jan 11, 2010 at 2:52 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Ramzi, > > > Ramzi TEMANNI wrote: > >> Hi, >> I'm runing some QC analysis with 5 Affy mouse genechip HT430PM >> I've installed the required libraries(affy, arrayQualityMetrics, >> htmg430pmcdf) and all dependecies >> I'm using the following code: >> fls <- list.files("/", ".*CEL") >> eset <- justRMA(filenames = fls) >> aBatch <- ReadAffy(filenames = fls) >> arrayQualityMetrics(aBatch,outdir = "report") >> >> The last commad shows the following error message: >> >> The report will be written in directory 'report'. >> Error in setQCEnvironment(cdfn) : >> Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy >> does not know the QC parameters for this array type. >> See the package vignette for details about how to specify QC parameters >> manually. >> > > This seems pretty clear to me. The simpleaffy package does not have the QC > parameters for this array and there is some explanation of how to fix this > in the package vignette. Did you look in the package vignette to see how to > fix it? > > Note that the htmg430pm chip is quite similar to the moe430 chip, so the QC > parameters will likely be the same, but you might need to adjust the names > of the QC probes. > > Best, > > Jim > > >> Error in density.default(as.matrix(log2(mm(expressionset))), ...) : >> 'x' contains missing values >> In addition: Warning message: >> In aqm.qcstats(expressionset) : >> 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. >> Error in obj[[i]]$legend : $ operator is invalid for atomic vectors >> In addition: Warning message: >> In arrayQualityMetrics(aBatch, outdir = "report") : >> Cannot draw the Perfect Match versus MisMatch plot >> >> Any idea about the orgin of this error ? >> Thanks in advance for your help. >> Kind regards >> Ramzi >> ---------------------------------------------------------------- >> >> sessionInfo() >>> >> R version 2.10.1 (2009-12-14) >> x86_64-pc-linux-gnu >> 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] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0 >> [3] preprocessCore_1.8.0 gcrma_2.18.0 >> [5] htmg430pmcdf_2.5.0 affy_1.24.2 >> [7] Biobase_2.6.1 >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 >> [4] beadarray_1.14.0 Biostrings_2.14.8 DBI_0.2-4 >> [7] genefilter_1.28.2 grid_2.10.1 hwriter_1.1 >> [10] IRanges_1.4.9 lattice_0.17-26 latticeExtra_0.6-4 >> [13] limma_3.2.1 marray_1.24.0 RColorBrewer_1.0-2 >> [16] RSQLite_0.7-3 simpleaffy_2.22.0 splines_2.10.1 >> [19] stats4_2.10.1 survival_2.35-8 tcltk_2.10.1 >> [22] tools_2.10.1 vsn_3.14.0 xtable_1.5-6 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > -- > 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 > [[alternative HTML version deleted]]