Hi Ivan,

Ivan Smirnov wrote:


> 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


I encountered what may be a similar problem. It relates to the format in which the AFE text output results files are saved (FULL, COMPACT, QC, MINIMAL). The package assumes/requires that the FULL format be used. I say this because the read.AgilentFE function specifically looks for the 'Sequence' column in the Features Table, and this is only included in the output file that is saved in the FULL format. You may have encountered another error prior to seeing this one, but your error message, as well as the file containing 'only' 27 columns, seems to indicate that your output file has been saved in other than the FULL format.

Good luck!
Derek
__________________________________________________
Derek Janszen, PhD
Biostatistician
Computational Biology & Bioinformatics
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN J4-33
Richland, WA  99352 USA
Tel:  509-372-4561
derek.janszen@pnl.gov



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