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

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

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