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 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 >> >> >> 12,15,20,21,22,25,26,27,31,32,33,34,38,39,40,43,44,45,48,49,50,54,55,59,60,64,65,69,70,73,74,75,78,79,83,84,88,89,90,94,95,96,97,100,101,102,106,107,108,110,111,112,114,116,117,118,119,120,121,122,125,127,131,132,135,136,139,142,143,144,146,147,148,149,151,152,154,156,158,159,160,161,162,165,167,168,171,172,173,179,180,181,182,183,184,187,190,191,196,197,198,199,205,206,207,208,211,213,217,218,219,221,222,224,227,228,230,232,234,237,238,241,242,246,249,252,253,254,255,257,259,260,263,264,266,267,269,270,271,273,275,276,279,281,283,285,288,292,294,296,298,301,304,307,309,310,312,315,316,317,321,324,326,329,332,333,334,336,339,341,343,345,346,348,351,352,353,354,357,358,360,367,369,370,372,373,375,376,378,381,383,384,385,386,388,389,391,392,394,395,397,400,403,404,405,407,410,412,415,419,421,424,426,427,429,430,432,434,436,437,439,441,443,446,449,452,454,456,457,458,461,465,468,470,471,472,474,475,477,480,483,486,490,491,493,495,498,501,504,506,507,509,510,512,513,5 >> [... 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@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@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]]