targets frame
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@giusy-della-gatta-3197
Last seen 8.1 years ago
Hi everybody, I am a beginner in the use of R for microarray normalization. I have Agilent two color microarray data, so I was thinking to use the Bioconductor LIMMA package to normalize my microarray by using loess method. In the first step there is the composition of a targets file. I did not undestand which kind of Agilent files I have to specify: they are asking to put in the filename column "the name of the image analysis output file" , which are the Agilent image analysis output file? Anybody can help me? Thank you Giu
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@kasper-daniel-hansen-2979
Last seen 11 days ago
United States
In the filename give it the name of the actual output file from Feature Extractor. That should be a big textfile, perhaps 30MB or more. Read the limma's Users Guide, see priscilla's email from today/ yesterday. She had almost the same question. Kasper On Dec 16, 2008, at 8:15 , Giusy Della Gatta wrote: > Hi everybody, > > I am a beginner in the use of R for microarray normalization. > I have Agilent two color microarray data, so I was thinking to use > the Bioconductor LIMMA package to normalize my microarray > by using loess method. > > In the first step there is the composition of a targets file. > I did not undestand which kind of Agilent files I have to specify: > they are asking to put in the filename column "the name of the image > analysis > output file" , which are the Agilent image analysis > output file? > > Anybody can help me? > > Thank you > Giu > > _______________________________________________ > 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
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@giusy-della-gatta-3197
Last seen 8.1 years ago
Thank you Kasper, I uploaded the file and I was trying to make the RG list but I got this message: > library (limma) > targets <- readTargets("target_frame_barc.txt") > RG <-read.maimages (targets$FileName, source="agilent") Error in read.maimages(targets$FileName, source = "agilent") : Must specify input files The file are in the same working directory and they are coming from agilent analysis, have I to specify something else? Thank you Giusy -----Original Message----- From: Kasper Daniel Hansen [mailto:khansen@stat.berkeley.edu] Sent: Tue 12/16/2008 12:08 PM To: Giusy Della Gatta Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] targets frame In the filename give it the name of the actual output file from Feature Extractor. That should be a big textfile, perhaps 30MB or more. Read the limma's Users Guide, see priscilla's email from today/ yesterday. She had almost the same question. Kasper On Dec 16, 2008, at 8:15 , Giusy Della Gatta wrote: > Hi everybody, > > I am a beginner in the use of R for microarray normalization. > I have Agilent two color microarray data, so I was thinking to use > the Bioconductor LIMMA package to normalize my microarray > by using loess method. > > In the first step there is the composition of a targets file. > I did not undestand which kind of Agilent files I have to specify: > they are asking to put in the filename column "the name of the image > analysis > output file" , which are the Agilent image analysis > output file? > > Anybody can help me? > > Thank you > Giu > > _______________________________________________ > 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