affyQCReport with drosgenome2cdf
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 21 days ago
Germany
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
affyQCReport affyQCReport • 1.5k views
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@james-w-macdonald-5106
Last seen 25 minutes ago
United States
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
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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 >
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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
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