[BioC] Agi4x44Preprocess - error on read.AgilentFE fucntion

Amanda F A Riccardi [guest] guest at bioconductor.org
Thu Jan 23 18:04:48 CET 2014

Hello everybody!

I'm using Agi4x44Preprocess package to deal with pre processing Agilent single color 4x44 whole mouse genome array, which data were obtained using feature extraction software.
 The problem is that I can't download my data with the function read.AgilentFE, I got an error - showed below - and the script just stop and, instead mine,  the author's example data is imported... I used read.maimages function of the package limma as an alternative, but I really would like to know what is wrong using read.AglentFE.

 -- output of sessionInfo(): 

> targets <- read.targets(infile="targets.txt")
Target File 
     FileName Treatment Gerep
CT1  CT1.txt        CT     1
CT2  CT2.txt        CT     1
CT3  CT3.txt        CT     1
TT1  TT1.txt        TT     2
TT2  TT2.txt        TT     2
TT3  TT3.txt        TT     2
PT1  PT1.txt        PT     3
PT2  PT2.txt        PT     3
PT3  PT3.txt        PT     3  

> dd <-read.AgilentFE(targets,makePLOT=TRUE)
Read CT1.txt 
Read CT2.txt 
Read CT3.txt 
Read TT1.txt 
Read TT2.txt 
Read TT3.txt 
Read PT1.txt 
Read PT2.txt 
Read PT3.txt 
 INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord 
Erro em read.AgilentFE(targets, makePLOT = TRUE) : 
   the script will stop now

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