Dear Mailing List, 

I have been struggling for some time with some agilent single channel arrays, which I believe has been scanned with a earlier version AFE, because they do not contain the columns Sequence and chr coord, but I have tried to use the Agi4x44PreProcess package, with some adjustments, please see below. My main problem now is that I cannot remove the agilent probe names which are embedded within the genesymbol column for some genes The reason for doing this is to prepare  files for GSEA analysis. The function for doing this in the Agi4x44PreProcess  package: gsea.files, does not work, porbably due the the columns I am lacking, and the filter.probes also returns an error message, probably due to the same reason. 

I would be very grateful for any comments and help

Thanks, 
Maria

Here is the code :

library("Agi4x44PreProcess")
library("hgug4112a.db")
library("vsn")
library("convert")
library("GO.db")

setwd("/mydirectory")

#reading targets file
targets=read.targets(infile="targets_ec3.txt")
targets[1:10,1:5]

names(targets)

#Many( has skipped them, but included FIleName, Treatment and GErep)

#read in files with LIMMA: 
dd <- read.maimages(targets$FileName, source="agilent", columns = list(G = "gMedianSignal", Gb = "gBGUsed", R = "gProcessedSignal",
   Rb = "gBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName","ProbeUID", "GeneName", 
   "SystematicName", "Description", "gIsWellAboveBG", "gIsFound", "gIsSaturated", "gIsFeatPopnOL", "gIsFeatNonUnifOL"))

#reads inn 146 arrays)

##########Quality control (skipped)

###########Background correction and normailzation and log 2 transformation:
library(vsn)
ddNORM = BGandNorm(dd, BGmethod = "half", NORMmethod = "quantile",foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)

#filtering: 
ddFILT=filter.probes(ddNORM,
                control=TRUE,
                wellaboveBG=TRUE,
                isfound=TRUE,
                wellaboveNEG=TRUE,
                sat=TRUE,
                PopnOL=TRUE,
                NonUnifOL=TRUE,
                nas=TRUE,
                limWellAbove=75,
                limISF=75,
                limNEG=75,
                limSAT=75,
                limPopnOL=75,
                limNonUnifOL=75,
                limNAS=100,
                makePLOT=TRUE,annotation.package="hgug4112a.db",flag.counts=FALSE,targets)

FILTERING PROBES BY FLAGS 


FILTERING BY ControlType FLAG 
Error in data.frame(PROBE_ID, as.character(probe.chr), as.character(probe.seq),  : 
  arguments imply differing number of rows: 43376, 0


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