[BioC] Limma question: readGenericHeader error message

[Gordon K Smyth]

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

> Date: Mon, 21 Nov 2011 17:35:07 -0500
> From: Ella Chang <ella7389 at hotmail.com>
> To: <bioconductor at r-project.org>
> Subject: [BioC] Limma question: readGenericHeader error message
>
>
> 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

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