Yisong, please search the archives, and post back if you still have problems: http://search.gmane.org/?query=qcdef cheers, Mark On 13/08/2008, at 1:49 PM, Yisong Zhen wrote: > Hi, > > I updated my R version and Bioconductor. But I met different error, > where > and how to set up ".qcdef" file? > > library(affy) > Tucson_data <- ReadAffy() > > library(affyQCReport); # Loads "affy" and "simpleaffy" packages > QCReport(Tucson_data, file="ExampleQC.pdf") > > setQCEnvironment(cdfn) : > Could not find array definition file ' cint06a520380fcdf.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. > >> sessionInfo() > R version 2.7.1 (2008-06-23) > i686-pc-linux-gnu > > locale: > LC_CTYPE > = > zh_CN > .GB18030 > ;LC_NUMERIC > = > C > ;LC_TIME > = > zh_CN > .GB18030 > ;LC_COLLATE > = > zh_CN > .GB18030 > ;LC_MONETARY > = > C > ;LC_MESSAGES > = > zh_CN > .GB18030 > ;LC_PAPER > = > zh_CN > .GB18030 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets > [8] methods base > > other attached packages: > [1] cint06a520380fcdf_1.18.0 affyQCReport_1.18.0 > geneplotter_1.18.0 > [4] annotate_1.18.0 AnnotationDbi_1.2.2 > RSQLite_0.6-9 > [7] DBI_0.2-4 lattice_0.17-8 > RColorBrewer_1.0-2 > [10] affyPLM_1.16.0 xtable_1.5-2 > simpleaffy_2.16.0 > [13] gcrma_2.12.1 matchprobes_1.12.0 > genefilter_1.20.0 > [16] survival_2.34-1 affy_1.18.2 > preprocessCore_1.2.1 > [19] affyio_1.8.1 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] grid_2.7.1 KernSmooth_2.22-22 > > I used same protocol to install the CDF file as before > > library(makecdfenv); > > make.cdf.package("CINT06a520380F.cdf ", species = > "Ciona_intestinalis"); > R CMD INSTALL cint06a520380fcdf > > I read the previous messages and they have similiar question but I > still do > not undstand why and how to proceed?? How to set the PATH variable? > > Thanks in advance. > > Yisong > > > > > On 8/12/08, Robert Gentleman <rgentlem at="" fhcrc.org=""> wrote: >> >> Hi Yisong, >> Your R is very out of date, and we don't fix problems that are that >> far >> back. Please update to R 2.7.1 (preferably patched) and try again, >> and then >> you will be able to get arrayQualityMetrics >> >> best wishes >> Robert >> >> >> Yisong Zhen wrote: >> >>> Dear Bioconductors and Robert, >>> >>> This is the output, >>> >>> (1) >>> >>>> Tucson_Array >>>> >>> AffyBatch object >>> size of arrays=716x716 features (8 kb) >>> cdf=CINT06a520380F (30969 affyids) >>> number of samples=5 >>> number of genes=30969 >>> annotation=cint06a520380f >>> notes= >>> >>> (2) >>> >>> sessionInfo() >>>> >>> R version 2.5.0 (2007-04-23) >>> i686-redhat-linux-gnu >>> >>> locale: >>> >>> LC_CTYPE >>> = >>> zh_CN >>> .GB18030 >>> ;LC_NUMERIC >>> = >>> C >>> ;LC_TIME >>> = >>> zh_CN >>> .GB18030 >>> ;LC_COLLATE >>> = >>> zh_CN >>> .GB18030 >>> ;LC_MONETARY >>> = >>> zh_CN >>> .GB18030 >>> ;LC_MESSAGES >>> = >>> zh_CN >>> .GB18030 >>> ;LC_PAPER >>> = >>> zh_CN >>> .GB18030 >>> ;LC_NAME >>> = >>> C >>> ;LC_ADDRESS >>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>> "datasets" >>> [7] "methods" "base" >>> >>> other attached packages: >>> affy affyio Biobase >>> "1.14.2" "1.4.1" "1.14.1" >>> (3) >>> When I try to install the arrayQualityMetrics, there is warning >>> message. I >>> cannot load the library arrayQualityMetrics. >>> >>> source("http://bioconductor.org/biocLite.R") >>>> biocLite("arrayQualityMetrics") >>>> >>> Running biocinstall version 2.0.8 with R version 2.5.0 >>> Your version of R requires version 2.0 of Bioconductor. >>> Warning message: >>> package 'arrayQualityMetrics' is not available in: >>> install.packages(pkgs = >>> pkgs, repos = repos, dependencies = dependencies, >>> >>> >>> Thanks. >>> >>> Yisong >>> >>> >>> On 8/12/08, Robert Gentleman <rgentlem at="" fhcrc.org=""> wrote: >>> >>>> Hi Yisong, >>>> >>>> Yisong Zhen wrote: >>>> >>>> Dear Bioconductors, >>>>> >>>>> I tried to get the quality control report generated by >>>>> affyQCReport. But >>>>> I >>>>> failed. >>>>> >>>>> This is my code: >>>>> >>>>> library(affy); >>>>> >>>>> Tucson_Array <-ReadAffy(); >>>>> >>>>> There is no need to have ; at the end of lines in R. >>>> >>>> Could you please post the output of sessionInfo(), as asked in the >>>> posting >>>> guide. Then try just >>>> >>>> Tucson_Array >>>> >>>> and let us know what happens. >>>> >>>> And finally, let me suggest that you try the arrayQualityMetrics >>>> package >>>> instead of using affyQCReport. The report it generates is a bit >>>> more >>>> comprehensive, but currently only in HTML (I think that will change >>>> soon). >>>> >>>> best wishes >>>> Robert >>>> >>>> >>>> library(affyQCReport); >>>>> QCReport(Tucson_Array, file="TucsonQC.pdf"); >>>>> >>>>> This is the error message: >>>>> >>>>> error density.default(newX[, i], ...) : >>>>> 'x' contains missing values >>>>> Warning message: >>>>> duplicate row.names >>>>> >>>>> >>>>> >>>>> 12,15,20,21,22,25,26,27,31,32,33,34,38,39,40,43,44,45,48,49,50,5 4,55,59,60,64,65,69,70,73,74,75,78,79,83,84,88,89,90,94,95,96,97,100,1 01,102,106,107,108,110,111,112,114,116,117,118,119,120,121,122,125,127 ,131,132,135,136,139,142,143,144,146,147,148,149,151,152,154,156,158,1 59,160,161,162,165,167,168,171,172,173,179,180,181,182,183,184,187,190 ,191,196,197,198,199,205,206,207,208,211,213,217,218,219,221,222,224,2 27,228,230,232,234,237,238,241,242,246,249,252,253,254,255,257,259,260 ,263,264,266,267,269,270,271,273,275,276,279,281,283,285,288,292,294,2 96,298,301,304,307,309,310,312,315,316,317,321,324,326,329,332,333,334 ,336,339,341,343,345,346,348,351,352,353,354,357,358,360,367,369,370,3 72,373,375,376,378,381,383,384,385,386,388,389,391,392,394,395,397,400 ,403,404,405,407,410,412,415,419,421,424,426,427,429,430,432,434,436,4 37,439,441,443,446,449,452,454,456,457,458,461,465,468,470,471,472,474 ,475,477,480,483,486,490,491,493,495,498,501,504,506,507,509,510,512,5 13,5 >>>>> [... truncated] in: data.row.names(row.names, rowsi, i) >>>>> >>>>> How can I do for next step to deal with the missing value and >>>>> duplicated >>>>> row.names? And what other packages (or steps) should I select to >>>>> assess >>>>> the >>>>> within-group variation so I can discard the poor quality array >>>>> (outlying >>>>> chips)? >>>>> >>>>> Thanks in advance. >>>>> >>>>> Yisong >>>>> >>>>> >>>>> >>>>> PS. >>>>> >>>>> And here is, >>>>> >>>>> sessionInfo() >>>>> R version 2.5.0 (2007-04-23) >>>>> i686-redhat-linux-gnu >>>>> >>>>> locale: >>>>> >>>>> >>>>> LC_CTYPE >>>>> = >>>>> zh_CN >>>>> .GB18030 >>>>> ;LC_NUMERIC >>>>> = >>>>> C >>>>> ;LC_TIME >>>>> = >>>>> zh_CN >>>>> .GB18030 >>>>> ;LC_COLLATE >>>>> = >>>>> zh_CN >>>>> .GB18030 >>>>> ;LC_MONETARY >>>>> = >>>>> zh_CN >>>>> .GB18030 >>>>> ;LC_MESSAGES >>>>> = >>>>> zh_CN >>>>> .GB18030 >>>>> ;LC_PAPER >>>>> = >>>>> zh_CN >>>>> .GB18030 >>>>> ;LC_NAME >>>>> = >>>>> C >>>>> ;LC_ADDRESS >>>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>>>> "datasets" >>>>> [7] "methods" "base" >>>>> >>>>> other attached packages: >>>>> cint06a520380fcdf affy affyio >>>>> Biobase >>>>> "1.14.0" "1.14.2" "1.4.1" >>>>> "1.14.1 >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>>> -- >>>> Robert Gentleman, PhD >>>> Program in Computational Biology >>>> Division of Public Health Sciences >>>> Fred Hutchinson Cancer Research Center >>>> 1100 Fairview Ave. N, M2-B876 >>>> PO Box 19024 >>>> Seattle, Washington 98109-1024 >>>> 206-667-7700 >>>> rgentlem at fhcrc.org >>>> >>>> >>> >>> >>> >> -- >> Robert Gentleman, PhD >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> PO Box 19024 >> Seattle, Washington 98109-1024 >> 206-667-7700 >> rgentlem at fhcrc.org >> > > > > -- > //------------------------------------------------------------------ ----------------------- > // We have a hunger of the mind which asks for knowledge > // of all around us, and the more we gain, the more is > // our desire; the more we see, the more we are capable > // of seeing. > //------------------------------------------------------------------ ---------------------- > > Yisong Zhen, Ph.D (Davidson Lab) > Molecular & Cellular Biology > Molecular Cardiovascular Research Program > University of Arizona > 1656 E. Mabel, MRB 317 > Tucson, AZ 85724 USA > Lab: 520-626-8153 > Cell: 520-977-7397 > > @------------------------------------------------------------------- -------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > 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