Reading flag data from Agilent files
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@giovanni-coppola-893
Last seen 10.2 years ago
Hello Frederic, you might be interested in this thread: http://article.gmane.org/gmane.science.biology.informatics.conductor/ 1822/ Best Giovanni On May 19, 2006, at 8:27 AM, Frederic Capel wrote: > Cher Monsieur, je viens demander un peu d'aide sur l'utilisation du > package Limma: j'esp?re que vous allez pouvoir m'aider! > je suis tomb? sur une question ancienne relative au flag de spots > lorsque > Limma est utilis? pour traiter des data issues de F extraction > d'agilent, > j'ai un souci comparable ? celui que vous aviez: je n'arrive pas ? > g?rer > les flags: pouvez vous me renseigner sur la commande ? introduire ? > dans > mon objet Rg je n'ai pas de weight, ce qui ?tait le cas lorsque je > travaillais avec Genepix et des .gpr > Merci par avance > > mon script pr?liminaire sans fonction pour les flags car rien ne > marche: > targets<- readTargets("target1.txt",row.names="Slide number") > RG <-read.maimages(targets$FileName,source="agilent") > #Read 251239140435.txt > #Read 251239140486.txt > #Read 251239140436.txt > #Read 251239140487.txt > #Read 251239140465.txt > #Read 251239140534.txt > #Read 251239140537.txt > #Read 251239140460.txt > #Read 251239140539.txt > #Read 251239140484.txt > #Read 251239143844.txt > #Read 251239140540.txt > > names(RG) > #[1] "G" "Gb" "R" "Rb" "targets" "genes" > "source" > names(RG$genes) > #[1] "Row" "Col" "ProbeUID" "ControlType" > #[5] "ProbeName" "GeneName" "SystematicName" "Description" > > > > > Votre message ?tait: > Hi list, > > does somebody here knows if there's a function in the > Bioconductor packages for reading flags data (feature > saturation, non uniformity, etc...) or other kind of > data from Agilent files (from Feature Extraction > software). I used read.Agilent(marray) but it doesn't > read other data that Fg and Bg intensities, wrong ? Or > is there something to do with the '... further > arguments to scan(base)' ? > > > > > > Frederic Capel, Ph D > PostDoc > INSERM U586, Obesity Research Unit > IFR31, Institut Louis Bugnard, BP 84225 > 31432 TOULOUSE Cedex 4 > Frederic.Capel at toulouse.inserm.fr > [[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
limma limma • 735 views
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