Question: help on reading Agilent 44k 2 colour
0
gravatar for Alberto Goldoni
9.7 years ago by
Alberto Goldoni60 wrote:
Dear all, i'm newbie in reading agilent 44k arrays. this is my targets file: "SlideNumber" "FileNameCy3" "FileNameCy5" "Cy3" "Cy5" 1 "prova01.txt" "prova02.txt" "WT" "Mutant" 2 "prova03.txt" "prova04.txt" "WT" "Mutant" 3 "prova05.txt" "prova06.txt" "WT" "Mutant" but readin in the limma user guide i'm not able to read the 6 chip > library("limma") > targets <- readTargets() > targets SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 prova01.txt prova02.txt WT Mutant 2 2 prova03.txt prova04.txt WT Mutant 3 3 prova05.txt prova06.txt WT Mutant > files <- targets[,c("FileNameCy3","FileNameCy5")] > files FileNameCy3 FileNameCy5 1 prova01.txt prova02.txt 2 prova03.txt prova04.txt 3 prova05.txt prova06.txt > RG <- read.maimages(files, source="imagene") Read header information Error in read.imagene(files = files, path = path, ext = ext, names = names, : Can't find Field Dimensions in ImaGene header In addition: Warning message: In readImaGeneHeader(fullname) : End of file encountered before End Header i know that "imagene" is not correct because i have used agilent Microarray Scanner (G2565CA) so i have the 6 txt files like the one that i have attached in the mail. is there anyone that can help me in reading this kind of microarrays? Best regards. ---------------------------------------- Alberto Goldoni, PhD IT Lan Manager Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy ----------------------------------------
genetics limma • 578 views
ADD COMMENTlink modified 9.7 years ago by Yong Li190 • written 9.7 years ago by Alberto Goldoni60
Answer: help on reading Agilent 44k 2 colour
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gravatar for Yong Li
9.7 years ago by
Yong Li190
Yong Li190 wrote:
Dear Alberto, as you know your files are from Agilent scanner you should use source="agilent" when calling read.maimages. Type ?read.maimages you will see details of how to use that function. A strange thing is that from your targets it seems you have one file for Cy3 and another file for Cy5. I never see Agilent 2 colour txt files like this. Normally one txt file for one chip, which includes both the Cy3 and Cy5 data. You might want to check this. Hope this helps. Yong On Wed, 17 Mar 2010 10:39:22 +0100 Alberto Goldoni <alberto.goldoni at="" segesta.pro=""> wrote: > > Dear all, > i'm newbie in reading agilent 44k arrays. > this is my targets file: > > "SlideNumber" "FileNameCy3" "FileNameCy5" "Cy3" "Cy5" > 1 "prova01.txt" "prova02.txt" "WT" "Mutant" > 2 "prova03.txt" "prova04.txt" "WT" "Mutant" > 3 "prova05.txt" "prova06.txt" "WT" "Mutant" > > but readin in the limma user guide i'm not able to read the 6 chip > > > library("limma") > > targets <- readTargets() > > targets > SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 > 1 1 prova01.txt prova02.txt WT Mutant > 2 2 prova03.txt prova04.txt WT Mutant > 3 3 prova05.txt prova06.txt WT Mutant > > files <- targets[,c("FileNameCy3","FileNameCy5")] > > files > FileNameCy3 FileNameCy5 > 1 prova01.txt prova02.txt > 2 prova03.txt prova04.txt > 3 prova05.txt prova06.txt > > RG <- read.maimages(files, source="imagene") > Read header information > Error in read.imagene(files = files, path = path, ext = ext, names = > names, : > Can't find Field Dimensions in ImaGene header > In addition: Warning message: > In readImaGeneHeader(fullname) : End of file encountered before End > Header > > > i know that "imagene" is not correct because i have used agilent > Microarray Scanner (G2565CA) so i have the 6 txt files like the one > that i have attached in the mail. > > is there anyone that can help me in reading this kind of microarrays? > > Best regards. > > ---------------------------------------- > Alberto Goldoni, PhD > IT Lan Manager > Medical Genetics Unit > S. Orsola-Malpighi Hospital > Via Massarenti n.9, Pad 11 > 40100 Bologna, Italy > ---------------------------------------- >
ADD COMMENTlink written 9.7 years ago by Yong Li190
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