marrayNorm - Getting Data Out
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@jean-yee-hwa-yang-104
Last seen 10.2 years ago
HI Michale, Try write.table(maM(data), file="data.xls", sep="\t", quote=FALSE) Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Thu, 31 Jul 2003, michael watson (IAH-C) wrote: > Hi > > This sounds kind of stupid, but if I have my data in an marrayNorm object, can anyone give any pointers on how to get it out into, say, a tab-delimited text file? > > Are there any special functions or is it simply write.table() ..?? > > Thanks > Mick > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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@james-w-macdonald-5106
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If you want your normalized log ratios, you can get them out of the marrayNorm object using the accessor function maM. For instance, if your marrayNorm object was called mydata, you would do something like: ratios <- maM(mydata) then write.table(ratios, ...) for more info, try ?marrayNorm HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> 07/31/03 06:16AM >>> Hi This sounds kind of stupid, but if I have my data in an marrayNorm object, can anyone give any pointers on how to get it out into, say, a tab-delimited text file? Are there any special functions or is it simply write.table() ..?? Thanks Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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@michael-watson-iah-c-378
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Great :-) I can use write.table() to get my normalised M values out into a tab delimited text file, but how do I also output the the spot annotations which I read in from my GAL file? Do I: - output my normalised M values using write.table() - output my spot annotations using maGnames(data) and write.table() - paste the two together in Excel or link them in Access? I can of course do the above, I just wondered if there was an output function that would basically output all of my normalised log ratios alongside all the spot annotations I read in to my marrayInfo object. Thanks Mick -----Original Message----- From: James MacDonald [mailto:jmacdon@med.umich.edu] Sent: 03 August 2003 04:37 To: michael.watson@bbsrc.ac.uk; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] marrayNorm - Getting Data Out If you want your normalized log ratios, you can get them out of the marrayNorm object using the accessor function maM. For instance, if your marrayNorm object was called mydata, you would do something like: ratios <- maM(mydata) then write.table(ratios, ...) for more info, try ?marrayNorm HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> 07/31/03 06:16AM >>> Hi This sounds kind of stupid, but if I have my data in an marrayNorm object, can anyone give any pointers on how to get it out into, say, a tab-delimited text file? Are there any special functions or is it simply write.table() ..?? Thanks Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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@michael-watson-iah-c-378
Last seen 10.2 years ago
OK, just to answer my own dumb question, it's something along the lines of: write.table(cbind(maGridRow(lowess.norm), maGridCol(lowess.norm), maSpotCol(lowess.norm), maSpotRow(lowess.norm), maM(lowess.norm)), file="C:\\test.txt") This will output grid location along with normalised M values for the marrayNorm object lowess.norm. If I have Gene Names in there, I can add maGnames(lowess.norm) to my list in the call to cbind() Thanks for your patience :-D -----Original Message----- From: michael watson (IAH-C) Sent: 05 August 2003 11:21 To: 'James MacDonald'; michael watson (IAH-C); bioconductor@stat.math.ethz.ch Subject: RE: [BioC] marrayNorm - Getting Data Out Great :-) I can use write.table() to get my normalised M values out into a tab delimited text file, but how do I also output the the spot annotations which I read in from my GAL file? Do I: - output my normalised M values using write.table() - output my spot annotations using maGnames(data) and write.table() - paste the two together in Excel or link them in Access? I can of course do the above, I just wondered if there was an output function that would basically output all of my normalised log ratios alongside all the spot annotations I read in to my marrayInfo object. Thanks Mick -----Original Message----- From: James MacDonald [mailto:jmacdon@med.umich.edu] Sent: 03 August 2003 04:37 To: michael.watson@bbsrc.ac.uk; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] marrayNorm - Getting Data Out If you want your normalized log ratios, you can get them out of the marrayNorm object using the accessor function maM. For instance, if your marrayNorm object was called mydata, you would do something like: ratios <- maM(mydata) then write.table(ratios, ...) for more info, try ?marrayNorm HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> 07/31/03 06:16AM >>> Hi This sounds kind of stupid, but if I have my data in an marrayNorm object, can anyone give any pointers on how to get it out into, say, a tab-delimited text file? Are there any special functions or is it simply write.table() ..?? Thanks Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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Hi Michael, There is method maGeneTable that will do that for you. write.table(cbind(maGeneTable(data), maM(data)), file="data.txt") Cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Tue, 5 Aug 2003, michael watson (IAH-C) wrote: > OK, just to answer my own dumb question, it's something along the lines of: > > write.table(cbind(maGridRow(lowess.norm), maGridCol(lowess.norm), > maSpotCol(lowess.norm), maSpotRow(lowess.norm), maM(lowess.norm)), > file="C:\\test.txt") > > This will output grid location along with normalised M values for the > marrayNorm object lowess.norm. If I have Gene Names in there, I can > add maGnames(lowess.norm) to my list in the call to cbind() > > Thanks for your patience :-D > > > -----Original Message----- > From: michael watson (IAH-C) > Sent: 05 August 2003 11:21 > To: 'James MacDonald'; michael watson (IAH-C); > bioconductor@stat.math.ethz.ch > Subject: RE: [BioC] marrayNorm - Getting Data Out > > > Great :-) > > I can use write.table() to get my normalised M values out into a tab delimited text file, but how do I also output the the spot annotations which I read in from my GAL file? > > Do I: > > - output my normalised M values using write.table() > - output my spot annotations using maGnames(data) and write.table() > - paste the two together in Excel or link them in Access? > > I can of course do the above, I just wondered if there was an output function that would basically output all of my normalised log ratios alongside all the spot annotations I read in to my marrayInfo object. > > Thanks > Mick > > -----Original Message----- > From: James MacDonald [mailto:jmacdon@med.umich.edu] > Sent: 03 August 2003 04:37 > To: michael.watson@bbsrc.ac.uk; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] marrayNorm - Getting Data Out > > > If you want your normalized log ratios, you can get them out of the > marrayNorm object using the accessor function maM. For instance, if your > marrayNorm object was called mydata, you would do something like: > > ratios <- maM(mydata) > then write.table(ratios, ...) > > for more info, try ?marrayNorm > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> 07/31/03 > 06:16AM >>> > Hi > > This sounds kind of stupid, but if I have my data in an marrayNorm > object, can anyone give any pointers on how to get it out into, say, a > tab-delimited text file? > > Are there any special functions or is it simply write.table() ..?? > > Thanks > Mick > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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