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Question: Problem reading ArrayVision files
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11.2 years ago by
Gordon Smyth33k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth33k wrote:
Dear Michael, > Date: Mon, 2 Apr 2007 13:44:50 -0400 > From: "michael waisberg" <waisberg at="" gmail.com=""> > Subject: [BioC] Problem reading ArrayVision files > To: bioconductor at stat.math.ethz.ch > > Hello, > > I've been trying to read and analyze some ArrayVision filesusing LIMMA and I > always get the same problem. I am using R 2.2.1 and I updated my LIMMA to > the last version today. Actually you're using a version of R which is about 15 months old, so you're getting an older version of limma as well. The only way to get the latest version of limma is to use the current version of R. I don't know what problem you have here exactly, without knowing your limma version and without seeing your input files. I can tell you that the reading of arrayvision files was broken by the introduction of colClasses into read.maimages() in limma 2.3.1 on 15 October 2005. colClasses greatly speaded up reading for most image analysis programs, but caused problems for a couple of the less common non-standard formats including ArrayVision. If you like, you can send me some of your input files and I'll continue to work on getting ArrayVision up again in limma. Best wishes Gordon > So far my code is very simple (the errors follow > below the code causing it): > >> targets <- readTargets("targets.txt") >> data <- read.maimages(targets$FileName, source="arrayvision") > > Read 01_WG_WR_600_900_flag.txt > Read 02_PG_PR_650_900_flag.txt > Read 03_PG_PR_650_900_flag.txt > Read 26_WG_WR_0651_flag.txt > Read 28_WG_WR_670_900.txt > Read 04_PG_PR_650_800.txt > Read 05_PG_PR_650_900.txt > Warning message: > number of items read is not a multiple of the number of columns > >> data$genes <- readGAL("cere32pinsJAN04.gal") >> data$printer <- getLayout(data$genes) >> MA<- normalizeWithinArrays(data, method="l") >> library(convert) >> data.marray <- as(data, "marrayRaw") > > Error in checkSlotAssignment(object, name, value) : > assignment of an object of class "integer" is not valid for slot 'maGf' in > an object of class "marrayRaw"; is(value, "matrix") is not TRUE > > When I try to normalize the data using a printtip method as for instance: >>MA<- normalizeWithinArrays(data) > I get the following error: > Error in switch(method, loess = { : printer layout information does not > match M row dimension > > The targets.txt file is like this: > SlideNumber FileName cy3 cy5 > 01 01_WG_WR_600_900_flag.txt WR WG > 02 02_PG_PR_650_900_flag.txt PR PG > 03 03_PG_PR_650_900_flag.txt PR PG > 26 26_WG_WR_0651_flag.txt WG WR > 28 28_WG_WR_670_900.txt WG WR > 04 04_PG_PR_650_800.txt PG PR > 05 05_PG_PR_650_900.txt PG PR > Anyone can help me? > > Best regards, > -- > Michael Waisberg > R. Nicaragua 443/701, Sion > Belo Horizonte, MG > Brazil > 30320-050 > > > _________________________________________ > "I do not fear computers. I fear the lack of them." > Isaac Asimov