Dear all, I am testing the 'arrayQualityMetrics' package with .CEL files obtained with Affymetrix Human Exon 1.0 ST Arrays as raw data. But, even though i got an html Qmreport, i also got these errors during the process on R: > Data <- ReadAffy() > Data@cdfName [1] "HuEx-1_0-st-v2" > Data AffyBatch object size of arrays=2560x2560 features (17 kb) cdf=HuEx-1_0-st-v2 (??? affyids) number of samples=2 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) > arrayQualityMetrics(expressionset = Data,outdir = "rawData_AQM",force = TRUE,d o.logtransform = TRUE) The report will be written into directory 'rawData_AQM'. Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available Error in fitPLM(pp1, background = FALSE, normalize = FALSE) : argument is try-error fitPLM requires AffyBatch Error in aqm.rle(expressionset, dataprep, affyproc, intgroup = intgroup) : trying to get slot "model.description" from an object (class "try- error") that is not an S4 object In addition: Warning message: In aqm.prepaffy(expressionset) : RLE and NUSE plots from the package 'affyPLM' cannot be produced for this data set. Error in aqm.nuse(expressionset, dataprep, affyproc, intgroup = intgroup) : trying to get slot "model.description" from an object (class "try- error") that is not an S4 object Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available > For more info: > sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.ISO-8859-1 LC_NUMERIC=C [3] LC_TIME=en_US.ISO-8859-1 LC_COLLATE=en_US.ISO-8859-1 [5] LC_MONETARY=C LC_MESSAGES=en_US.ISO-8859-1 [7] LC_PAPER=en_US.ISO-8859-1 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.ISO-8859-1 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 [3] affyPLM_1.26.1 preprocessCore_1.12.0 [5] gcrma_2.22.0 affy_1.28.0 [7] Biobase_2.10.0 R.utils_1.7.4 [9] R.oo_1.8.0 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0 [4] beadarray_2.0.5 Biostrings_2.18.4 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 [10] IRanges_1.8.9 KernSmooth_2.23-4 lattice_0.19-17 [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 [19] splines_2.12.2 stats4_2.12.2 survival_2.36-5 [22] SVGAnnotation_0.9-0 tools_2.12.2 XML_3.2-0 [25] xtable_1.5-6 It seems that there is some kind of problem with the AffyBatch object i generated (called 'Data' in the example attached). The problem could be the annotation? I also searched for the 'huex10stv2cdf' package unsuccessfully. In a normal html report with Affymetrix arrays i obtained: * Section 1: Individual array quality <file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s1="" #s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s1#s1=""> * MA plots * Spatial distribution of feature intensities * Section 2: Array intensity distributions <file: c:\documents="" %20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.ht="" ml#s2#s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escrito="" rio\rawdata_aqm_affy\qmreport.html#s2#s2=""> * Boxplots * Density plots <file: c:\documents%20and%20settings\nqueralt.hcp\es="" critorio\rawdata_aqm_affy\qmreport.html#s3#s3=""> * Section 3: Between array comparison <file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s3="" #s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s3#s3=""> * Heatmap representation of the distances between arrays * Principal Component Analysis * Section 4: Variance mean dependence <file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s4="" #s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s4#s4=""> * Standard deviation versus rank of the mean * Section 5: Affymetrix specific plots <file: c:\documents%20a="" nd%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s="" 5#s5=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\="" rawdata_aqm_affy\qmreport.html#s5#s5=""> * RNA digestion plot * Relative Log Expression plot * Normalized Unscaled Standard Error (NUSE) plot * Diagnostic plot recommended by Affymetrix * Perfect matches and mismatches And with the exon array: * Section 1: Individual array quality <file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s1#s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s1#s1=""> * MA plots * Spatial distribution of feature intensities * Section 2: Array intensity distributions <file: c:\documents="" %20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s2="" #s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm\qmreport.html#s2#s2=""> * Boxplots * Density plots * Section 3: Between array comparison <file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s3#s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s3#s3=""> * Heatmap representation of the distances between arrays * Principal Component Analysis * Section 4: Variance mean dependence <file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s4#s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s4#s4=""> * Standard deviation versus rank of the mean * Section 5: Affymetrix specific plots <file: c:\documents%20a="" nd%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s5#s5=""> Nothing in the last section as you can see. The rest of the sections look normal. What am i doing wrong? Many thanks in advance! Regards, ------------------------------------------------------- Núria [[alternative HTML version deleted]]

Hi N?ria, The arrayQualityMetrics package relies on the affy and simpleaffy packages for much of the data processing. Unfortunately, neither of these packages is designed for a non 3'-biased array like the exon chip. You want to use either oligo or xps for these data, or if you want to go off-campus, the aroma.affymetrix package will work as well. Best, Jim On 4/6/2011 9:37 AM, nqueralt at clinic.ub.es wrote: > Dear all, > > > > I am testing the 'arrayQualityMetrics' package with .CEL files obtained with Affymetrix Human Exon 1.0 ST Arrays as raw data. But, even though i got an html Qmreport, i also got these errors during the process on R: > > > >> Data<- ReadAffy() > >> Data at cdfName > > [1] "HuEx-1_0-st-v2" > >> Data > > AffyBatch object > > size of arrays=2560x2560 features (17 kb) > > cdf=HuEx-1_0-st-v2 (??? affyids) > > number of samples=2 > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > In addition: Warning message: > > missing cdf environment! in show(AffyBatch) > >> arrayQualityMetrics(expressionset = Data,outdir = "rawData_AQM",force = TRUE,d o.logtransform = TRUE) > > The report will be written into directory 'rawData_AQM'. > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > Error in fitPLM(pp1, background = FALSE, normalize = FALSE) : > > argument is try-error fitPLM requires AffyBatch > > Error in aqm.rle(expressionset, dataprep, affyproc, intgroup = intgroup) : > > trying to get slot "model.description" from an object (class "try-error") that is not an S4 object > > In addition: Warning message: > > In aqm.prepaffy(expressionset) : > > RLE and NUSE plots from the package 'affyPLM' cannot be produced for this data set. > > Error in aqm.nuse(expressionset, dataprep, affyproc, intgroup = intgroup) : > > trying to get slot "model.description" from an object (class "try-error") that is not an S4 object > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > >> > > > > > > For more info: > > > >> sessionInfo() > > R version 2.12.2 (2011-02-25) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.ISO-8859-1 LC_NUMERIC=C > > [3] LC_TIME=en_US.ISO-8859-1 LC_COLLATE=en_US.ISO-8859-1 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.ISO-8859-1 > > [7] LC_PAPER=en_US.ISO-8859-1 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.ISO-8859-1 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices datasets utils methods base > > > > other attached packages: > > [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 > > [3] affyPLM_1.26.1 preprocessCore_1.12.0 > > [5] gcrma_2.22.0 affy_1.28.0 > > [7] Biobase_2.10.0 R.utils_1.7.4 > > [9] R.oo_1.8.0 R.methodsS3_1.2.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0 > > [4] beadarray_2.0.5 Biostrings_2.18.4 DBI_0.2-5 > > [7] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 > > [10] IRanges_1.8.9 KernSmooth_2.23-4 lattice_0.19-17 > > [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 > > [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 > > [19] splines_2.12.2 stats4_2.12.2 survival_2.36-5 > > [22] SVGAnnotation_0.9-0 tools_2.12.2 XML_3.2-0 > > [25] xtable_1.5-6 > > > > It seems that there is some kind of problem with the AffyBatch object i generated (called 'Data' in the example attached). The problem could be the annotation? I also searched for the 'huex10stv2cdf' package unsuccessfully. > > In a normal html report with Affymetrix arrays i obtained: > > > > * Section 1: Individual array quality<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s1#="" s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s1#s1=""> > > * MA plots > * Spatial distribution of feature intensities > > > > * Section 2: Array intensity distributions<file: c:\documents%="" 20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.htm="" l#s2#s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escrito="" rio\rawdata_aqm_affy\qmreport.html#s2#s2=""> > > * Boxplots > * Density plots > <file: c:\documents%20and%20settings\nqueralt.hcp\es="" critorio\rawdata_aqm_affy\qmreport.html#s3#s3=""> > > * Section 3: Between array comparison<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s3#="" s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s3#s3=""> > > * Heatmap representation of the distances between arrays > * Principal Component Analysis > > > > * Section 4: Variance mean dependence<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s4#="" s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s4#s4=""> > > * Standard deviation versus rank of the mean > > > > * Section 5: Affymetrix specific plots<file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s5="" #s5=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\="" rawdata_aqm_affy\qmreport.html#s5#s5=""> > > * RNA digestion plot > * Relative Log Expression plot > * Normalized Unscaled Standard Error (NUSE) plot > * Diagnostic plot recommended by Affymetrix > * Perfect matches and mismatches > > And with the exon array: > > > > * Section 1: Individual array quality<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s1#s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s1#s1=""> > > * MA plots > * Spatial distribution of feature intensities > > > > * Section 2: Array intensity distributions<file: c:\documents%="" 20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s2#="" s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm\qmreport.html#s2#s2=""> > > * Boxplots > * Density plots > > > > * Section 3: Between array comparison<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s3#s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s3#s3=""> > > * Heatmap representation of the distances between arrays > * Principal Component Analysis > > > > * Section 4: Variance mean dependence<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s4#s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s4#s4=""> > > * Standard deviation versus rank of the mean > > > > * Section 5: Affymetrix specific plots<file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s5#s5=""> > > > > Nothing in the last section as you can see. The rest of the sections look normal. What am i doing wrong? > > > > > > Many thanks in advance! > > > > Regards, > > > > ------------------------------------------------------- > N?ria > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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

Dear N?ria, On April 14 the new Bioconductor version 2.8 will be released. This version will contain an updated version of package "xps" which does contain (almost) all quality controls described in the "arrayQualityMetrics" package, including RNA degradation plots, for Exon ST and Gene ST arrays. Currently you can download it from the developer branch of BioC. Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 4/6/11 3:37 PM, nqueralt at clinic.ub.es wrote: > Dear all, > > > > I am testing the 'arrayQualityMetrics' package with .CEL files obtained with Affymetrix Human Exon 1.0 ST Arrays as raw data. But, even though i got an html Qmreport, i also got these errors during the process on R: > > > >> Data<- ReadAffy() > >> Data at cdfName > > [1] "HuEx-1_0-st-v2" > >> Data > > AffyBatch object > > size of arrays=2560x2560 features (17 kb) > > cdf=HuEx-1_0-st-v2 (??? affyids) > > number of samples=2 > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > In addition: Warning message: > > missing cdf environment! in show(AffyBatch) > >> arrayQualityMetrics(expressionset = Data,outdir = "rawData_AQM",force = TRUE,d o.logtransform = TRUE) > > The report will be written into directory 'rawData_AQM'. > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > Error in fitPLM(pp1, background = FALSE, normalize = FALSE) : > > argument is try-error fitPLM requires AffyBatch > > Error in aqm.rle(expressionset, dataprep, affyproc, intgroup = intgroup) : > > trying to get slot "model.description" from an object (class "try-error") that is not an S4 object > > In addition: Warning message: > > In aqm.prepaffy(expressionset) : > > RLE and NUSE plots from the package 'affyPLM' cannot be produced for this data set. > > Error in aqm.nuse(expressionset, dataprep, affyproc, intgroup = intgroup) : > > trying to get slot "model.description" from an object (class "try-error") that is not an S4 object > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > >> > > > > > > For more info: > > > >> sessionInfo() > > R version 2.12.2 (2011-02-25) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.ISO-8859-1 LC_NUMERIC=C > > [3] LC_TIME=en_US.ISO-8859-1 LC_COLLATE=en_US.ISO-8859-1 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.ISO-8859-1 > > [7] LC_PAPER=en_US.ISO-8859-1 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.ISO-8859-1 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices datasets utils methods base > > > > other attached packages: > > [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 > > [3] affyPLM_1.26.1 preprocessCore_1.12.0 > > [5] gcrma_2.22.0 affy_1.28.0 > > [7] Biobase_2.10.0 R.utils_1.7.4 > > [9] R.oo_1.8.0 R.methodsS3_1.2.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0 > > [4] beadarray_2.0.5 Biostrings_2.18.4 DBI_0.2-5 > > [7] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 > > [10] IRanges_1.8.9 KernSmooth_2.23-4 lattice_0.19-17 > > [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 > > [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 > > [19] splines_2.12.2 stats4_2.12.2 survival_2.36-5 > > [22] SVGAnnotation_0.9-0 tools_2.12.2 XML_3.2-0 > > [25] xtable_1.5-6 > > > > It seems that there is some kind of problem with the AffyBatch object i generated (called 'Data' in the example attached). The problem could be the annotation? I also searched for the 'huex10stv2cdf' package unsuccessfully. > > In a normal html report with Affymetrix arrays i obtained: > > > > * Section 1: Individual array quality<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s1#="" s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s1#s1=""> > > * MA plots > * Spatial distribution of feature intensities > > > > * Section 2: Array intensity distributions<file: c:\documents%="" 20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.htm="" l#s2#s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escrito="" rio\rawdata_aqm_affy\qmreport.html#s2#s2=""> > > * Boxplots > * Density plots > <file: c:\documents%20and%20settings\nqueralt.hcp\es="" critorio\rawdata_aqm_affy\qmreport.html#s3#s3=""> > > * Section 3: Between array comparison<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s3#="" s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s3#s3=""> > > * Heatmap representation of the distances between arrays > * Principal Component Analysis > > > > * Section 4: Variance mean dependence<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s4#="" s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s4#s4=""> > > * Standard deviation versus rank of the mean > > > > * Section 5: Affymetrix specific plots<file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s5="" #s5=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\="" rawdata_aqm_affy\qmreport.html#s5#s5=""> > > * RNA digestion plot > * Relative Log Expression plot > * Normalized Unscaled Standard Error (NUSE) plot > * Diagnostic plot recommended by Affymetrix > * Perfect matches and mismatches > > And with the exon array: > > > > * Section 1: Individual array quality<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s1#s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s1#s1=""> > > * MA plots > * Spatial distribution of feature intensities > > > > * Section 2: Array intensity distributions<file: c:\documents%="" 20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s2#="" s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm\qmreport.html#s2#s2=""> > > * Boxplots > * Density plots > > > > * Section 3: Between array comparison<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s3#s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s3#s3=""> > > * Heatmap representation of the distances between arrays > * Principal Component Analysis > > > > * Section 4: Variance mean dependence<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s4#s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s4#s4=""> > > * Standard deviation versus rank of the mean > > > > * Section 5: Affymetrix specific plots<file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s5#s5=""> > > > > Nothing in the last section as you can see. The rest of the sections look normal. What am i doing wrong? > > > > > > Many thanks in advance! > > > > Regards, > > > > ------------------------------------------------------- > N?ria > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Nuria generally, please use the (soon-to-be-released) devel version of arrayQualityMetrics, it should deal more gracefully with your array type and makes a much nicer report. If there is no CDF file, the Affymetrix-specific quality metrics that are based on probesets (NUSE, RLE, RNA 'digestion') will obviously not work, but everyhing else should. Please let me know if you have any problems with that (best to provide a small example dataset and the script that you ran). Best wishes Wolfgang Il Apr/6/11 3:37 PM, nqueralt at clinic.ub.es ha scritto: > Dear all, > > > > I am testing the 'arrayQualityMetrics' package with .CEL files obtained with Affymetrix Human Exon 1.0 ST Arrays as raw data. But, even though i got an html Qmreport, i also got these errors during the process on R: > > > >> Data<- ReadAffy() > >> Data at cdfName > > [1] "HuEx-1_0-st-v2" > >> Data > > AffyBatch object > > size of arrays=2560x2560 features (17 kb) > > cdf=HuEx-1_0-st-v2 (??? affyids) > > number of samples=2 > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > In addition: Warning message: > > missing cdf environment! in show(AffyBatch) > >> arrayQualityMetrics(expressionset = Data,outdir = "rawData_AQM",force = TRUE,d o.logtransform = TRUE) > > The report will be written into directory 'rawData_AQM'. > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > Error in fitPLM(pp1, background = FALSE, normalize = FALSE) : > > argument is try-error fitPLM requires AffyBatch > > Error in aqm.rle(expressionset, dataprep, affyproc, intgroup = intgroup) : > > trying to get slot "model.description" from an object (class "try-error") that is not an S4 object > > In addition: Warning message: > > In aqm.prepaffy(expressionset) : > > RLE and NUSE plots from the package 'affyPLM' cannot be produced for this data set. > > Error in aqm.nuse(expressionset, dataprep, affyproc, intgroup = intgroup) : > > trying to get slot "model.description" from an object (class "try-error") that is not an S4 object > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain HuEx-1_0-st-v2 > > Library - package huex10stv2cdf not installed > > Bioconductor - huex10stv2cdf not available > >> > > > > > > For more info: > > > >> sessionInfo() > > R version 2.12.2 (2011-02-25) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.ISO-8859-1 LC_NUMERIC=C > > [3] LC_TIME=en_US.ISO-8859-1 LC_COLLATE=en_US.ISO-8859-1 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.ISO-8859-1 > > [7] LC_PAPER=en_US.ISO-8859-1 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.ISO-8859-1 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices datasets utils methods base > > > > other attached packages: > > [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 > > [3] affyPLM_1.26.1 preprocessCore_1.12.0 > > [5] gcrma_2.22.0 affy_1.28.0 > > [7] Biobase_2.10.0 R.utils_1.7.4 > > [9] R.oo_1.8.0 R.methodsS3_1.2.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0 > > [4] beadarray_2.0.5 Biostrings_2.18.4 DBI_0.2-5 > > [7] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 > > [10] IRanges_1.8.9 KernSmooth_2.23-4 lattice_0.19-17 > > [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 > > [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1 > > [19] splines_2.12.2 stats4_2.12.2 survival_2.36-5 > > [22] SVGAnnotation_0.9-0 tools_2.12.2 XML_3.2-0 > > [25] xtable_1.5-6 > > > > It seems that there is some kind of problem with the AffyBatch object i generated (called 'Data' in the example attached). The problem could be the annotation? I also searched for the 'huex10stv2cdf' package unsuccessfully. > > In a normal html report with Affymetrix arrays i obtained: > > > > * Section 1: Individual array quality<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s1#="" s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s1#s1=""> > > * MA plots > * Spatial distribution of feature intensities > > > > * Section 2: Array intensity distributions<file: c:\documents%="" 20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.htm="" l#s2#s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escrito="" rio\rawdata_aqm_affy\qmreport.html#s2#s2=""> > > * Boxplots > * Density plots > <file: c:\documents%20and%20settings\nqueralt.hcp\es="" critorio\rawdata_aqm_affy\qmreport.html#s3#s3=""> > > * Section 3: Between array comparison<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s3#="" s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s3#s3=""> > > * Heatmap representation of the distances between arrays > * Principal Component Analysis > > > > * Section 4: Variance mean dependence<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s4#="" s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm_affy\qmreport.html#s4#s4=""> > > * Standard deviation versus rank of the mean > > > > * Section 5: Affymetrix specific plots<file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm_affy\qmreport.html#s5="" #s5=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\="" rawdata_aqm_affy\qmreport.html#s5#s5=""> > > * RNA digestion plot > * Relative Log Expression plot > * Normalized Unscaled Standard Error (NUSE) plot > * Diagnostic plot recommended by Affymetrix > * Perfect matches and mismatches > > And with the exon array: > > > > * Section 1: Individual array quality<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s1#s1=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s1#s1=""> > > * MA plots > * Spatial distribution of feature intensities > > > > * Section 2: Array intensity distributions<file: c:\documents%="" 20and%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s2#="" s2=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\r="" awdata_aqm\qmreport.html#s2#s2=""> > > * Boxplots > * Density plots > > > > * Section 3: Between array comparison<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s3#s3=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s3#s3=""> > > * Heatmap representation of the distances between arrays > * Principal Component Analysis > > > > * Section 4: Variance mean dependence<file: c:\documents%20and="" %20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s4#s4=""> <file: c:\documents%20and%20settings\nqueralt.hcp\escritorio\rawdata="" _aqm\qmreport.html#s4#s4=""> > > * Standard deviation versus rank of the mean > > > > * Section 5: Affymetrix specific plots<file: c:\documents%20an="" d%20settings\nqueralt.hcp\escritorio\rawdata_aqm\qmreport.html#s5#s5=""> > > > > Nothing in the last section as you can see. The rest of the sections look normal. What am i doing wrong? > > > > > > Many thanks in advance! > > > > Regards, > > > > ------------------------------------------------------- > N?ria > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber