[BioC] Agi4x44PreProcess Problem

[Smirnov, Ivan]

Hi Pedro,

I was trying to use your package Agi4x44PreProcess and getting an error when calling:

dd=read.AgilentFE(targ, makePLOT=FALSE)

Error in readGenericHeader(fullname, columns = columns, sep = sep) :
  Specified column headings not found in file
Calls: read.AgilentFE -> read.maimages -> readGenericHeader

I checked Bioconductor list, this problem has been reported last month, but not resolved so far, AFAIK.

I am using the latest R/Bioconductor on Linux. The target files are produced by the scanner G2505C using Feature Extractor v. 10.5.1.1. The files have 27 columns:

TYPE  FEATURES
integer  FeatureNum
integer  Row
integer  Col
integer  SubTypeMask
integer  ControlType
text  ProbeName
text  SystematicName
float PositionX
float PositionY
float gProcessedSignal
float gProcessedSigError
float gMedianSignal
float gBGMedianSignal
float gBGPixSDev
boolean  gIsSaturated
boolean  gIsLowPMTScaledUp
boolean  gIsFeatNonUnifOL
boolean  gIsBGNonUnifOL
boolean  gIsFeatPopnOL
boolean  gIsBGPopnOL
boolean  IsManualFlag
float gBGSubSignal
boolean  gIsPosAndSignif
boolean  gIsWellAboveBG
float SpotExtentX
float gBGMeanSignal

Please help!

Thanks for sharing your code!

Ivan