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Limma question: readGenericHeader error message

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Ella Chang ▴ 20

@ella-chang-4969

Last seen 9.7 years ago

Hi all, I am trying to load my agilent data to Limma using read.maimages function. Here's what I did: > library(limma)> targets<-readTargets("targets.txt")> RG <- read.maimages(targets, columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal",+ Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName")) but I got the error message says: Read US83000170_252018610364_S01_GE2_105_Dec08_1_3.txt Read US83000170_252018610364_S01_GE2_105_Dec08_1_4.txt Read US83000170_252018610386_S01_GE2_105_Dec08_1_2.txt Read US83000170_252018610386_S01_GE2_105_Dec08_1_4.txt Error in readGenericHeader(fullname, columns = columns) : Specified column headings not found in fileIn addition: Warning message:In file(file, "r") : file("") only supports open = "w+" and open = "w+b": using the former I already checked to made sure that all the columns I specified are existed in all my file. Does anyone know how to deal with this? thanks a lot for your help HC [[alternative HTML version deleted]]

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ADD COMMENT • link updated 12.5 years ago by Gordon Smyth 50k • written 12.5 years ago by Ella Chang ▴ 20

score 0 · Answer 1 · 2011-11-23

Dear Ella,

I have just tried out the read.maimages() call sequence you have used on an Agilent file that I have, and it works perfectly. So I do not know the problem you have.

From the output you give, read.maimages() has successfully read your first four files, but has failed on the fifth. So it would seem that the specified columns are not contained in all of your files. The fifth file specified in your targets data.frame is the culprit.

BTW, what you want to do is a bit more easily achieved by

   RG <- read.maimages(targets,source="agilent.median")

although I suspect it will give the same results as you already have.

If you post again, please give sessionInfo() output.

Best wishes
Gordon