Chromosome 23 and 24 dropped after run snapCGH processCGH
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@caiweimdandersonorg-1599
Last seen 7.1 years ago
Dear list, I am using snapCGH to look at Agilent's mouse aCGH array. my MAlist object (MA1) have chromosomes 1-19, 23 and 24. After I run the processCGH function, chromosome 23 and 24 are no longer in my new MAlist object (MA2). Any idea where the problem is? Thanks! __________________________ Caimiao Wei, Ph.D. Senior Statistical Analyst Division of Quantitative Sciences UT M.D.Anderson Cancer Center 1515 Holcombe Blvd, Unit 237 Houston, TX 77030-4009 Tel: (713)563-4297 Fax: (713) 792-4262 Office location: HMB13. 200A > table(MA1$genes$Chr) 1 2 3 4 5 6 7 8 9 10 11 12 13 16283 16856 13062 13658 13977 14156 13570 11538 12058 11879 12658 10443 10693 14 15 16 17 18 19 23 24 10836 9357 9090 9122 8092 6405 12089 612 > MA2<-processCGH(MA1, method.of.averaging=NULL, ID='ProbeName') > table(MA2$genes$Chr) 1 2 3 4 5 6 7 8 9 10 11 12 13 16283 16856 13062 13658 13977 14156 13570 11538 12058 11879 12658 10443 10693 14 15 16 17 18 19 10836 9357 9090 9122 8092 6405 > sessionInfo() R version 2.5.1 (2007-06-27) sparc-sun-solaris2.9 locale: C attached base packages: [1] "splines" "grid" "tools" "stats" "graphics" "grDevices" [7] "utils" "datasets" "methods" "base" other attached packages: xtable snapCGH aCGH sma multtest cluster "1.4-6" "1.4.0" "1.10.0" "0.5.15" "1.16.0" "1.11.7" GLAD aws DNAcopy tilingArray pixmap geneplotter "1.10.0" "1.3-3.1" "1.10.0" "1.14.0" "0.4-7" "1.14.0" lattice annotate genefilter survival vsn strucchange "0.15-11" "1.14.1" "1.14.1" "2.32" "2.2.0" "1.3-2" sandwich zoo RColorBrewer affy affyio Biobase "2.0-2" "1.3-2" "1.0-1" "1.14.2" "1.4.1" "1.14.1" limma "2.10.5" >
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@sean-davis-490
Last seen 6 weeks ago
United States
caiwei at mdanderson.org wrote: > Dear list, > > I am using snapCGH to look at Agilent's mouse aCGH array. my MAlist object > (MA1) have chromosomes 1-19, 23 and 24. After I run the processCGH > function, chromosome 23 and 24 are no longer in my new MAlist object (MA2). > > Any idea where the problem is? Thanks! The help for processCGH will answer that question. In short, the maxChromThreshold argument has a default of 22. Sean
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J-C. Marioni ▴ 40
@j-c-marioni-2033
Last seen 7.1 years ago
Hi Caimiao, If you set the argument maxChromThreshold equal to 24, this should prevent chromosomes 23 and 24 being excluded from the MA object. Hope this helps, John On Wed, 3 Oct 2007, caiwei at mdanderson.org wrote: > Dear list, > > I am using snapCGH to look at Agilent's mouse aCGH array. my MAlist object > (MA1) have chromosomes 1-19, 23 and 24. After I run the processCGH > function, chromosome 23 and 24 are no longer in my new MAlist object (MA2). > > Any idea where the problem is? Thanks! > > > __________________________ > Caimiao Wei, Ph.D. > > Senior Statistical Analyst > Division of Quantitative Sciences > UT M.D.Anderson Cancer Center > 1515 Holcombe Blvd, Unit 237 > Houston, TX 77030-4009 > > Tel: (713)563-4297 > Fax: (713) 792-4262 > Office location: HMB13. 200A > > > >> table(MA1$genes$Chr) > > 1 2 3 4 5 6 7 8 9 10 11 12 > 13 > 16283 16856 13062 13658 13977 14156 13570 11538 12058 11879 12658 10443 > 10693 > 14 15 16 17 18 19 23 24 > 10836 9357 9090 9122 8092 6405 12089 612 > >> MA2<-processCGH(MA1, method.of.averaging=NULL, ID='ProbeName') >> table(MA2$genes$Chr) > > 1 2 3 4 5 6 7 8 9 10 11 12 > 13 > 16283 16856 13062 13658 13977 14156 13570 11538 12058 11879 12658 10443 > 10693 > 14 15 16 17 18 19 > 10836 9357 9090 9122 8092 6405 >> sessionInfo() > R version 2.5.1 (2007-06-27) > sparc-sun-solaris2.9 > > locale: > C > > attached base packages: > [1] "splines" "grid" "tools" "stats" "graphics" > "grDevices" > [7] "utils" "datasets" "methods" "base" > > other attached packages: > xtable snapCGH aCGH sma multtest > cluster > "1.4-6" "1.4.0" "1.10.0" "0.5.15" "1.16.0" > "1.11.7" > GLAD aws DNAcopy tilingArray pixmap > geneplotter > "1.10.0" "1.3-3.1" "1.10.0" "1.14.0" "0.4-7" > "1.14.0" > lattice annotate genefilter survival vsn > strucchange > "0.15-11" "1.14.1" "1.14.1" "2.32" "2.2.0" > "1.3-2" > sandwich zoo RColorBrewer affy affyio > Biobase > "2.0-2" "1.3-2" "1.0-1" "1.14.2" "1.4.1" > "1.14.1" > limma > "2.10.5" >> > > _______________________________________________ > 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 >