Question

Agi4x44PreProcess Problem

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Smirnov, Ivan ▴ 10

@smirnov-ivan-4069

Last seen 10.4 years ago

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

Agi4x44PreProcess Agi4x44PreProcess • 1.3k views

ADD COMMENT • link updated 14.7 years ago by Janszen, Derek B ▴ 10 • written 14.7 years ago by Smirnov, Ivan ▴ 10

score 0 · Answer 1 · 2010-05-11

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 [[alternative HTML version deleted]]