The function read.AgilentFE has not been designed to directly read data from
miRNA. The error message you get is due to the fact that I included on
purpose a stop point if the "Sequence and chr_coord" cannot be found in the
input data set, in order to avoid using the function to read other data
different from the one that the function is expecting to get. You can use
this function, instead, which is similar to read.AgilentFE :

read.microRNA.AgilentFE <- function(targets){
 if (!is(targets, "data.frame")){
        stop("'targets' must be a data.frame")
 }
  ddaux=read.maimages(files=targets$FileName,source="agilent",
            other.columns=list(IsGeneDetected="gIsGeneDetected",
            IsSaturated="gIsSaturated",
            IsFeatNonUnifOF="gIsFeatNonUnifOL",
            IsFeatPopnOL="gIsFeatPopnOL",
            ChrCoord="chr_coord",
            BGKmd="gBGMedianSignal",
            BGKus="gBGUsed"),
          columns=list(Rf="gTotalGeneSignal",
            Gf="gTotalProbeSignal",
            Rb="gMeanSignal",
            Gb="gProcessedSignal"),
          verbose=T,sep="\t",quote="")
        dd=new("RGList")
                dd$R=ddaux$R
                dd$G=ddaux$G
                dd$Rb=ddaux$Rb
                dd$Gb=ddaux$Gb
                dd$targets=ddaux$targets
                dd$genes=ddaux$genes[,c(4,5,6)]
                dd$other=ddaux$other
        rm(ddaux)
  cat("","\n")
  cat("  RGList:","\n")
  cat(" dd$R:  'gTotalGeneSignal' ","\n")
  cat(" dd$G:  'gTotalProbeSignal' ","\n")
  cat(" dd$Rb:  'gMeanSignal' ","\n")
  cat(" dd$Gb:  'gProcessedSignal' ","\n")
  cat("","\n")
return(dd)
} # end function

HTH

pedro



Hi all,

is there any way to get the Agi4x44PreProcess package working with Agilent
miRNA data? I have a target object pointing at Agilent txt files
containing miRNA data. Reading mRNA data is no problem. For miRNA data I
get the following error:

> dd=read.AgilentFE(targets, makePLOT=FALSE)
Read ***.txt
Read ***.txt
...
INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord
SCANN THE DATA USING AFE 9.5.3.1
Error in read.AgilentFE(targets, makePLOT = FALSE) :
   the script will stop now

Any suggestions?

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