Question: read.table(), then use affycoretools?
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gravatar for Weiyin Zhou
12.9 years ago by
Weiyin Zhou220
Weiyin Zhou220 wrote:
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ADD COMMENTlink modified 12.9 years ago • written 12.9 years ago by Weiyin Zhou220
Answer: read.table(), then use affycoretools?
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gravatar for James W. MacDonald
12.9 years ago by
United States
James W. MacDonald52k wrote:
Hi Weiyin, Weiyin Zhou wrote: > Hi James, > > > > I use read.table() to read .txt file, which have 7 columns (probeID, 3 > columns for control, next 3 for ko). These data have already rma > pre-processed. Here is the first ten lines after I used read.table: > > > > >>data <- read.table("Apopt_rma.txt", header=TRUE, row.names="ID") > > >>data[1:10,] > > > Eurasnet.Apoptosis.CEL Eurasnet.Apoptosis2.CEL > > AFFX-BioB-3_at 10.16030 9.75900 > > AFFX-BioB-5_at 9.56744 9.07906 > > AFFX-BioB-M_at 10.38530 9.94925 > > AFFX-BioC-3_at 10.30660 9.81339 > > AFFX-BioC-5_at 10.97160 10.54450 > > AFFX-BioDn-3_at 12.43740 12.17020 > > AFFX-BioDn-5_at 11.80980 11.45310 > > AFFX-CreX-3_at 13.76850 13.67820 > > AFFX-CreX-5_at 13.59800 13.48740 > > AFFX-DapX-3_at 7.58850 8.05139 > > Eurasnet.Apoptosis3.CEL Eurasnet.Apoptosis4.CEL > > AFFX-BioB-3_at 9.61602 9.43489 > > AFFX-BioB-5_at 9.02821 8.83341 > > AFFX-BioB-M_at 9.85227 9.69166 > > AFFX-BioC-3_at 9.75543 9.62851 > > AFFX-BioC-5_at 10.42980 10.27400 > > AFFX-BioDn-3_at 12.00490 12.00640 > > AFFX-BioDn-5_at 11.29640 11.35080 > > AFFX-CreX-3_at 13.48130 13.68150 > > AFFX-CreX-5_at 13.26550 13.44120 > > AFFX-DapX-3_at 7.06897 6.90034 > > Eurasnet.Apoptosis5.CEL Eurasnet.Apoptosis6.CEL > > AFFX-BioB-3_at 10.29660 9.69907 > > AFFX-BioB-5_at 9.72952 9.08717 > > AFFX-BioB-M_at 10.59420 9.92486 > > AFFX-BioC-3_at 10.47480 9.89643 > > AFFX-BioC-5_at 11.15980 10.54430 > > AFFX-BioDn-3_at 12.58160 12.18040 > > AFFX-BioDn-5_at 12.12000 11.58860 > > AFFX-CreX-3_at 13.86080 13.81650 > > AFFX-CreX-5_at 13.78710 13.67390 > > AFFX-DapX-3_at 7.07626 7.12627 > > > > My phenoData is; > > >>pd <- read.phenoData("pData.txt", header=TRUE, row.names=1) > > >>show(pData(pd)) > > > Target > > Eurasnet-Apoptosis1.CEL CO > > Eurasnet-Apoptosis2.CEL CO > > Eurasnet-Apoptosis3.CEL CO > > Eurasnet-Apoptosis4.CEL KO > > Eurasnet-Apoptosis5.CEL KO > > Eurasnet-Apoptosis6.CEL KO > > > > Can I doing some sort of conversion for the data from output of > read.table, to make data object look like the eset object you create > from affystart(), combine with phenoData info, so I can use it to call > lmFit () and other function in limma package. > For the current BioC release, you can create an exprSet like this: eset <- new("exprSet", exprs = as.matrix(Data), phenoData = pd) You might get an error because your phenoData row.names are not the same as the colnames of your Data object. If so, you might have to change the row names first. row.names(pd) <- sub("-", ".", row.names(pd)) Note that this won't work with R-2.5.0/BioC 2.0. In that case you will have to create an ExpressionSet, and your pd object has to be read in using read.AnnotatedDataFrame(). HTH, Jim > > > Thanks in advance, > > Regards, > > Weiyin Zhou > > Statistics and Data Analyst > > ExonHit Therapeutics, Inc. > > 217 Perry Parkway, Building # 5 > > Gaithersburg, MD 20877 > > > > email: Weiyin.zhou at exonhit-usa.com <mailto: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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.9 years ago by James W. MacDonald52k
Answer: read.table(), then use affycoretools?
0
gravatar for Weiyin Zhou
12.9 years ago by
Weiyin Zhou220
Weiyin Zhou220 wrote:
Hi James, Thanks! I get the error message when I try: > eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd) Error in validObject(.Object) : invalid class "exprSet" object: sampleNames different from names of phenoData rows So I try below code, but get another error message: > row.names(pd) <- sub("-", ".", row.names(pd)) Error in `rownames<-`(x, value) : attempt to set rownames on object with no dimensions Here is my seesionInfo: > 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: affycoretools biomaRt RCurl XML GOstats "1.6.0" "1.8.1" "0.8-0" "1.4-0" "2.0.4" Category genefilter survival KEGG RBGL "2.0.3" "1.12.0" "2.30" "1.12.0" "1.10.0" annotate GO graph limma affy "1.12.0" "1.14.1" "1.12.0" "2.9.1" "1.12.2" affyio Biobase "1.2.0" "1.12.2" Thanks, Weiyin -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Tuesday, January 09, 2007 10:28 AM To: Weiyin Zhou Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] read.table(), then use affycoretools? Hi Weiyin, Weiyin Zhou wrote: > Hi James, > > > > I use read.table() to read .txt file, which have 7 columns (probeID, 3 > columns for control, next 3 for ko). These data have already rma > pre-processed. Here is the first ten lines after I used read.table: > > > > >>data <- read.table("Apopt_rma.txt", header=TRUE, row.names="ID") > > >>data[1:10,] > > > Eurasnet.Apoptosis.CEL Eurasnet.Apoptosis2.CEL > > AFFX-BioB-3_at 10.16030 9.75900 > > AFFX-BioB-5_at 9.56744 9.07906 > > AFFX-BioB-M_at 10.38530 9.94925 > > AFFX-BioC-3_at 10.30660 9.81339 > > AFFX-BioC-5_at 10.97160 10.54450 > > AFFX-BioDn-3_at 12.43740 12.17020 > > AFFX-BioDn-5_at 11.80980 11.45310 > > AFFX-CreX-3_at 13.76850 13.67820 > > AFFX-CreX-5_at 13.59800 13.48740 > > AFFX-DapX-3_at 7.58850 8.05139 > > Eurasnet.Apoptosis3.CEL Eurasnet.Apoptosis4.CEL > > AFFX-BioB-3_at 9.61602 9.43489 > > AFFX-BioB-5_at 9.02821 8.83341 > > AFFX-BioB-M_at 9.85227 9.69166 > > AFFX-BioC-3_at 9.75543 9.62851 > > AFFX-BioC-5_at 10.42980 10.27400 > > AFFX-BioDn-3_at 12.00490 12.00640 > > AFFX-BioDn-5_at 11.29640 11.35080 > > AFFX-CreX-3_at 13.48130 13.68150 > > AFFX-CreX-5_at 13.26550 13.44120 > > AFFX-DapX-3_at 7.06897 6.90034 > > Eurasnet.Apoptosis5.CEL Eurasnet.Apoptosis6.CEL > > AFFX-BioB-3_at 10.29660 9.69907 > > AFFX-BioB-5_at 9.72952 9.08717 > > AFFX-BioB-M_at 10.59420 9.92486 > > AFFX-BioC-3_at 10.47480 9.89643 > > AFFX-BioC-5_at 11.15980 10.54430 > > AFFX-BioDn-3_at 12.58160 12.18040 > > AFFX-BioDn-5_at 12.12000 11.58860 > > AFFX-CreX-3_at 13.86080 13.81650 > > AFFX-CreX-5_at 13.78710 13.67390 > > AFFX-DapX-3_at 7.07626 7.12627 > > > > My phenoData is; > > >>pd <- read.phenoData("pData.txt", header=TRUE, row.names=1) > > >>show(pData(pd)) > > > Target > > Eurasnet-Apoptosis1.CEL CO > > Eurasnet-Apoptosis2.CEL CO > > Eurasnet-Apoptosis3.CEL CO > > Eurasnet-Apoptosis4.CEL KO > > Eurasnet-Apoptosis5.CEL KO > > Eurasnet-Apoptosis6.CEL KO > > > > Can I doing some sort of conversion for the data from output of > read.table, to make data object look like the eset object you create > from affystart(), combine with phenoData info, so I can use it to call > lmFit () and other function in limma package. > For the current BioC release, you can create an exprSet like this: eset <- new("exprSet", exprs = as.matrix(Data), phenoData = pd) You might get an error because your phenoData row.names are not the same as the colnames of your Data object. If so, you might have to change the row names first. row.names(pd) <- sub("-", ".", row.names(pd)) Note that this won't work with R-2.5.0/BioC 2.0. In that case you will have to create an ExpressionSet, and your pd object has to be read in using read.AnnotatedDataFrame(). HTH, Jim > > > Thanks in advance, > > Regards, > > Weiyin Zhou > > Statistics and Data Analyst > > ExonHit Therapeutics, Inc. > > 217 Perry Parkway, Building # 5 > > Gaithersburg, MD 20877 > > > > email: Weiyin.zhou at exonhit-usa.com <mailto: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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.9 years ago by Weiyin Zhou220
Hmm, yeah. Sorry about that. S4 and stuff ;-D How about a <- pData(pd) row.names(a) <- sub("-",".", row.names(a)) pData(pd) <- a and then proceed. Alternatively you can modify the text file before running read.phenoData(). Best, Jim Weiyin Zhou wrote: > Hi James, > > Thanks! > > I get the error message when I try: > >>eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd) > > Error in validObject(.Object) : invalid class "exprSet" object: > sampleNames different from names of phenoData rows > > So I try below code, but get another error message: > >>row.names(pd) <- sub("-", ".", row.names(pd)) > > Error in `rownames<-`(x, value) : attempt to set rownames on object with > no dimensions > > > Here is my seesionInfo: > >>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: > affycoretools biomaRt RCurl XML GOstats > "1.6.0" "1.8.1" "0.8-0" "1.4-0" "2.0.4" > Category genefilter survival KEGG RBGL > "2.0.3" "1.12.0" "2.30" "1.12.0" "1.10.0" > annotate GO graph limma affy > "1.12.0" "1.14.1" "1.12.0" "2.9.1" "1.12.2" > affyio Biobase > "1.2.0" "1.12.2" > > > > > Thanks, > > Weiyin > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Tuesday, January 09, 2007 10:28 AM > To: Weiyin Zhou > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] read.table(), then use affycoretools? > > Hi Weiyin, > > Weiyin Zhou wrote: > >>Hi James, >> >> >> >>I use read.table() to read .txt file, which have 7 columns (probeID, 3 >>columns for control, next 3 for ko). These data have already rma >>pre-processed. Here is the first ten lines after I used read.table: >> >> >> >> >> >>>data <- read.table("Apopt_rma.txt", header=TRUE, row.names="ID") >> >> >>>data[1:10,] >> >> >> Eurasnet.Apoptosis.CEL Eurasnet.Apoptosis2.CEL >> >>AFFX-BioB-3_at 10.16030 9.75900 >> >>AFFX-BioB-5_at 9.56744 9.07906 >> >>AFFX-BioB-M_at 10.38530 9.94925 >> >>AFFX-BioC-3_at 10.30660 9.81339 >> >>AFFX-BioC-5_at 10.97160 10.54450 >> >>AFFX-BioDn-3_at 12.43740 12.17020 >> >>AFFX-BioDn-5_at 11.80980 11.45310 >> >>AFFX-CreX-3_at 13.76850 13.67820 >> >>AFFX-CreX-5_at 13.59800 13.48740 >> >>AFFX-DapX-3_at 7.58850 8.05139 >> >> Eurasnet.Apoptosis3.CEL Eurasnet.Apoptosis4.CEL >> >>AFFX-BioB-3_at 9.61602 9.43489 >> >>AFFX-BioB-5_at 9.02821 8.83341 >> >>AFFX-BioB-M_at 9.85227 9.69166 >> >>AFFX-BioC-3_at 9.75543 9.62851 >> >>AFFX-BioC-5_at 10.42980 10.27400 >> >>AFFX-BioDn-3_at 12.00490 12.00640 >> >>AFFX-BioDn-5_at 11.29640 11.35080 >> >>AFFX-CreX-3_at 13.48130 13.68150 >> >>AFFX-CreX-5_at 13.26550 13.44120 >> >>AFFX-DapX-3_at 7.06897 6.90034 >> >> Eurasnet.Apoptosis5.CEL Eurasnet.Apoptosis6.CEL >> >>AFFX-BioB-3_at 10.29660 9.69907 >> >>AFFX-BioB-5_at 9.72952 9.08717 >> >>AFFX-BioB-M_at 10.59420 9.92486 >> >>AFFX-BioC-3_at 10.47480 9.89643 >> >>AFFX-BioC-5_at 11.15980 10.54430 >> >>AFFX-BioDn-3_at 12.58160 12.18040 >> >>AFFX-BioDn-5_at 12.12000 11.58860 >> >>AFFX-CreX-3_at 13.86080 13.81650 >> >>AFFX-CreX-5_at 13.78710 13.67390 >> >>AFFX-DapX-3_at 7.07626 7.12627 >> >> >> >>My phenoData is; >> >> >> >>>pd <- read.phenoData("pData.txt", header=TRUE, row.names=1) >> >> >>>show(pData(pd)) >> >> >> Target >> >>Eurasnet-Apoptosis1.CEL CO >> >>Eurasnet-Apoptosis2.CEL CO >> >>Eurasnet-Apoptosis3.CEL CO >> >>Eurasnet-Apoptosis4.CEL KO >> >>Eurasnet-Apoptosis5.CEL KO >> >>Eurasnet-Apoptosis6.CEL KO >> >> >> >>Can I doing some sort of conversion for the data from output of >>read.table, to make data object look like the eset object you create >>from affystart(), combine with phenoData info, so I can use it to call >>lmFit () and other function in limma package. >> > > > For the current BioC release, you can create an exprSet like this: > > eset <- new("exprSet", exprs = as.matrix(Data), phenoData = pd) > > You might get an error because your phenoData row.names are not the same > > as the colnames of your Data object. If so, you might have to change the > > row names first. > > row.names(pd) <- sub("-", ".", row.names(pd)) > > Note that this won't work with R-2.5.0/BioC 2.0. In that case you will > have to create an ExpressionSet, and your pd object has to be read in > using read.AnnotatedDataFrame(). > > > HTH, > > Jim > > > > > >> >> >>Thanks in advance, >> >>Regards, >> >>Weiyin Zhou >> >>Statistics and Data Analyst >> >>ExonHit Therapeutics, Inc. >> >>217 Perry Parkway, Building # 5 >> >>Gaithersburg, MD 20877 >> >> >> >>email: Weiyin.zhou at exonhit-usa.com > > <mailto: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 > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 12.9 years ago by James W. MacDonald52k
Answer: read.table(), then use affycoretools?
0
gravatar for Weiyin Zhou
12.9 years ago by
Weiyin Zhou220
Weiyin Zhou220 wrote:
James, I modified my pData.txt file, so it works now. It is kind weird. I checked my "Apop_ram.txt", the column names are match with row names in pData.txt. But somehow, when read.table, it changed "-" to ".". And I did not even noticed at beginning. Thanks a lot, Weiyin -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Tuesday, January 09, 2007 11:05 AM To: Weiyin Zhou Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] read.table(), then use affycoretools? Hmm, yeah. Sorry about that. S4 and stuff ;-D How about a <- pData(pd) row.names(a) <- sub("-",".", row.names(a)) pData(pd) <- a and then proceed. Alternatively you can modify the text file before running read.phenoData(). Best, Jim Weiyin Zhou wrote: > Hi James, > > Thanks! > > I get the error message when I try: > >>eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd) > > Error in validObject(.Object) : invalid class "exprSet" object: > sampleNames different from names of phenoData rows > > So I try below code, but get another error message: > >>row.names(pd) <- sub("-", ".", row.names(pd)) > > Error in `rownames<-`(x, value) : attempt to set rownames on object with > no dimensions > > > Here is my seesionInfo: > >>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: > affycoretools biomaRt RCurl XML GOstats > "1.6.0" "1.8.1" "0.8-0" "1.4-0" "2.0.4" > Category genefilter survival KEGG RBGL > "2.0.3" "1.12.0" "2.30" "1.12.0" "1.10.0" > annotate GO graph limma affy > "1.12.0" "1.14.1" "1.12.0" "2.9.1" "1.12.2" > affyio Biobase > "1.2.0" "1.12.2" > > > > > Thanks, > > Weiyin > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Tuesday, January 09, 2007 10:28 AM > To: Weiyin Zhou > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] read.table(), then use affycoretools? > > Hi Weiyin, > > Weiyin Zhou wrote: > >>Hi James, >> >> >> >>I use read.table() to read .txt file, which have 7 columns (probeID, 3 >>columns for control, next 3 for ko). These data have already rma >>pre-processed. Here is the first ten lines after I used read.table: >> >> >> >> >> >>>data <- read.table("Apopt_rma.txt", header=TRUE, row.names="ID") >> >> >>>data[1:10,] >> >> >> Eurasnet.Apoptosis.CEL Eurasnet.Apoptosis2.CEL >> >>AFFX-BioB-3_at 10.16030 9.75900 >> >>AFFX-BioB-5_at 9.56744 9.07906 >> >>AFFX-BioB-M_at 10.38530 9.94925 >> >>AFFX-BioC-3_at 10.30660 9.81339 >> >>AFFX-BioC-5_at 10.97160 10.54450 >> >>AFFX-BioDn-3_at 12.43740 12.17020 >> >>AFFX-BioDn-5_at 11.80980 11.45310 >> >>AFFX-CreX-3_at 13.76850 13.67820 >> >>AFFX-CreX-5_at 13.59800 13.48740 >> >>AFFX-DapX-3_at 7.58850 8.05139 >> >> Eurasnet.Apoptosis3.CEL Eurasnet.Apoptosis4.CEL >> >>AFFX-BioB-3_at 9.61602 9.43489 >> >>AFFX-BioB-5_at 9.02821 8.83341 >> >>AFFX-BioB-M_at 9.85227 9.69166 >> >>AFFX-BioC-3_at 9.75543 9.62851 >> >>AFFX-BioC-5_at 10.42980 10.27400 >> >>AFFX-BioDn-3_at 12.00490 12.00640 >> >>AFFX-BioDn-5_at 11.29640 11.35080 >> >>AFFX-CreX-3_at 13.48130 13.68150 >> >>AFFX-CreX-5_at 13.26550 13.44120 >> >>AFFX-DapX-3_at 7.06897 6.90034 >> >> Eurasnet.Apoptosis5.CEL Eurasnet.Apoptosis6.CEL >> >>AFFX-BioB-3_at 10.29660 9.69907 >> >>AFFX-BioB-5_at 9.72952 9.08717 >> >>AFFX-BioB-M_at 10.59420 9.92486 >> >>AFFX-BioC-3_at 10.47480 9.89643 >> >>AFFX-BioC-5_at 11.15980 10.54430 >> >>AFFX-BioDn-3_at 12.58160 12.18040 >> >>AFFX-BioDn-5_at 12.12000 11.58860 >> >>AFFX-CreX-3_at 13.86080 13.81650 >> >>AFFX-CreX-5_at 13.78710 13.67390 >> >>AFFX-DapX-3_at 7.07626 7.12627 >> >> >> >>My phenoData is; >> >> >> >>>pd <- read.phenoData("pData.txt", header=TRUE, row.names=1) >> >> >>>show(pData(pd)) >> >> >> Target >> >>Eurasnet-Apoptosis1.CEL CO >> >>Eurasnet-Apoptosis2.CEL CO >> >>Eurasnet-Apoptosis3.CEL CO >> >>Eurasnet-Apoptosis4.CEL KO >> >>Eurasnet-Apoptosis5.CEL KO >> >>Eurasnet-Apoptosis6.CEL KO >> >> >> >>Can I doing some sort of conversion for the data from output of >>read.table, to make data object look like the eset object you create >>from affystart(), combine with phenoData info, so I can use it to call >>lmFit () and other function in limma package. >> > > > For the current BioC release, you can create an exprSet like this: > > eset <- new("exprSet", exprs = as.matrix(Data), phenoData = pd) > > You might get an error because your phenoData row.names are not the same > > as the colnames of your Data object. If so, you might have to change the > > row names first. > > row.names(pd) <- sub("-", ".", row.names(pd)) > > Note that this won't work with R-2.5.0/BioC 2.0. In that case you will > have to create an ExpressionSet, and your pd object has to be read in > using read.AnnotatedDataFrame(). > > > HTH, > > Jim > > > > > >> >> >>Thanks in advance, >> >>Regards, >> >>Weiyin Zhou >> >>Statistics and Data Analyst >> >>ExonHit Therapeutics, Inc. >> >>217 Perry Parkway, Building # 5 >> >>Gaithersburg, MD 20877 >> >> >> >>email: Weiyin.zhou at exonhit-usa.com > > <mailto: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 > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.9 years ago by Weiyin Zhou220
Weiyin Zhou wrote: > James, > > I modified my pData.txt file, so it works now. > > It is kind weird. I checked my "Apop_ram.txt", the column names are > match with row names in pData.txt. But somehow, when read.table, it > changed "-" to ".". And I did not even noticed at beginning. There are certain characters that are disallowed (-, +, *, /, =, are a few that I know of) in the names of a data.frame. These are all converted to a ".", so you have to watch out for that. Best, Jim > > Thanks a lot, > > Weiyin -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 12.9 years ago by James W. MacDonald52k
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