Question: Agilent's one color array
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12.5 years ago by
Weiyin Zhou220
Weiyin Zhou220 wrote:
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ADD COMMENTlink modified 12.5 years ago • written 12.5 years ago by Weiyin Zhou220
Answer: Agilent's one color array
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gravatar for Weiwei Shi
12.5 years ago by
Weiwei Shi1.2k
Weiwei Shi1.2k wrote:
can you just use newData = as.matrix(data[, 2:5]) rownames(newData) = data[, 1] So your rownames contain ID you need. HTH, Weiwei On 6/14/07, Weiyin Zhou <weiyin.zhou at="" exonhit-usa.com=""> wrote: > Dear listers, > > > > I am analyzing Agilent's one-color array. I use limma package to read > data then do quantile normalization between arrays on RG$G and log2 the > data. Then I try to convert the data to exprSet object so I can > analyzing it the way similar to Affmetrix array. > > > > > data[1:5,] > > ID File1 File2 File3 File4 File5 File6 > > 1 A_15_P100001 9.92 9.91 9.86 10.07 10.03 9.86 > > 2 A_15_P100002 9.40 9.20 8.81 8.82 8.89 8.94 > > 3 A_15_P100003 4.08 3.67 3.32 2.47 2.89 2.91 > > 4 A_15_P100004 2.30 2.41 2.51 2.81 2.68 2.57 > > 5 A_15_P100005 11.29 11.38 11.25 10.94 11.06 11.29 > > > > > pd <- read.phenoData("pData.txt", header=TRUE, row.names=1) > > > show(pData(pd)) > > Target > > File1 group1 > > File2 group1 > > File3 group1 > > File4 group2 > > File5 group2 > > File6 group2 > > > > > eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd) > > Error in validObject(.Object) : invalid class "exprSet" object: 1: > number of exprs columns different from number of pData rows > > invalid class "exprSet" object: 2: sampleNames different from names of > phenoData rows > > > > I know the problem is because the ID column. Is there any way I can > only read data starting from second column(File1) but also associate the > result with ID later on? > > > > > sessionInfo() > > R version 2.4.0 (2006-10-03) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "splines" "tools" "methods" "stats" "graphics" > "grDevices" > > [7] "utils" "datasets" "base" > > > > other attached packages: > > biomaRt RCurl XML GOstats Category genefilter > survival > > "1.8.1" "0.8-0" "1.4-0" "2.0.4" "2.0.3" "1.12.0" > "2.30" > > KEGG RBGL annotate GO graph affy > affyio > > "1.12.0" "1.10.0" "1.12.0" "1.14.1" "1.12.0" "1.12.2" > "1.2.0" > > Biobase limma > > "1.12.2" "2.9.1" > > > > > > Thanks in advance, > > > > Weiyin > > > > > > > > Weiyin Zhou > > Senior Research Associate > > ExonHit Therapeutics, Inc. > > 217 Perry Parkway, Building # 5 > > Gaithersburg, MD 20877 > > > > email: Weiyin.zhou at exonhit-usa.com > > phone: 240.404.0184 > > fax: 240.683.7060 > > > > > [[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 > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III
ADD COMMENTlink written 12.5 years ago by Weiwei Shi1.2k
Answer: Agilent's one color array
0
gravatar for Weiyin Zhou
12.5 years ago by
Weiyin Zhou220
Weiyin Zhou220 wrote:
It works. Thanks, Weiwei. Weiyin -----Original Message----- From: Weiwei Shi [mailto:helprhelp@gmail.com] Sent: Thursday, June 14, 2007 4:36 PM To: Weiyin Zhou Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Agilent's one color array can you just use newData = as.matrix(data[, 2:5]) rownames(newData) = data[, 1] So your rownames contain ID you need. HTH, Weiwei On 6/14/07, Weiyin Zhou <weiyin.zhou at="" exonhit-usa.com=""> wrote: > Dear listers, > > > > I am analyzing Agilent's one-color array. I use limma package to read > data then do quantile normalization between arrays on RG$G and log2 the > data. Then I try to convert the data to exprSet object so I can > analyzing it the way similar to Affmetrix array. > > > > > data[1:5,] > > ID File1 File2 File3 File4 File5 File6 > > 1 A_15_P100001 9.92 9.91 9.86 10.07 10.03 9.86 > > 2 A_15_P100002 9.40 9.20 8.81 8.82 8.89 8.94 > > 3 A_15_P100003 4.08 3.67 3.32 2.47 2.89 2.91 > > 4 A_15_P100004 2.30 2.41 2.51 2.81 2.68 2.57 > > 5 A_15_P100005 11.29 11.38 11.25 10.94 11.06 11.29 > > > > > pd <- read.phenoData("pData.txt", header=TRUE, row.names=1) > > > show(pData(pd)) > > Target > > File1 group1 > > File2 group1 > > File3 group1 > > File4 group2 > > File5 group2 > > File6 group2 > > > > > eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd) > > Error in validObject(.Object) : invalid class "exprSet" object: 1: > number of exprs columns different from number of pData rows > > invalid class "exprSet" object: 2: sampleNames different from names of > phenoData rows > > > > I know the problem is because the ID column. Is there any way I can > only read data starting from second column(File1) but also associate the > result with ID later on? > > > > > sessionInfo() > > R version 2.4.0 (2006-10-03) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "splines" "tools" "methods" "stats" "graphics" > "grDevices" > > [7] "utils" "datasets" "base" > > > > other attached packages: > > biomaRt RCurl XML GOstats Category genefilter > survival > > "1.8.1" "0.8-0" "1.4-0" "2.0.4" "2.0.3" "1.12.0" > "2.30" > > KEGG RBGL annotate GO graph affy > affyio > > "1.12.0" "1.10.0" "1.12.0" "1.14.1" "1.12.0" "1.12.2" > "1.2.0" > > Biobase limma > > "1.12.2" "2.9.1" > > > > > > Thanks in advance, > > > > Weiyin > > > > > > > > Weiyin Zhou > > Senior Research Associate > > ExonHit Therapeutics, Inc. > > 217 Perry Parkway, Building # 5 > > Gaithersburg, MD 20877 > > > > email: Weiyin.zhou at exonhit-usa.com > > phone: 240.404.0184 > > fax: 240.683.7060 > > > > > [[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 > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III
ADD COMMENTlink written 12.5 years ago by Weiyin Zhou220
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