[BioC] Loading data into AgiMicroRna

[Steve Taylor]

Hi again,

>
> I am copying the mail from Pedro to the mailing list. I am thinking if
> you can read the files using read.maimages function it should work.
>

I have loaded my data in AgiMicroRna using:

dd=read.maimages(files=targets.micro$FileName,source="agilent",
     columns=list(Rf="gTotalGeneSignal",
     Gf="gTotalProbeSignal",
     Rb="gMedianSignal",
     Gb="gProcessedSignal"),
     other.columns=list(IsGeneDetected="gIsGeneDetected",
     IsSaturated="gIsSaturated",
     IsFeatNonUnifOF="gIsFeatNonUnifOL",
     IsFeatPopnOL="gIsFeatPopnOL",
     BGKmd="gBGMedianSignal"),
     annotation = c( "ControlType", "ProbeName"),
     verbose=TRUE,sep="\t",quote="")


There was no Rb="gMeanSignal", but I assume this should be ok.

Everything looked ok until I tried to normalize the data.

> ddTGS = tgsMicroRna(dd.micro, half = TRUE, makePLOT = FALSE,verbose = FALSE)
> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = FALSE,makePLOTpost = FALSE, targets.micro, verbose = TRUE)
Error in xy.coords(x, y) : 'x' and 'y' lengths differ

I see this problem has come up before on the list:

http://article.gmane.org/gmane.science.biology.informatics.conductor/31182/match=xy+coords+x+y+lengths+differ+agimicrorna

But I was wondering if there is a solution for it?  Apologies if I have missed something.

Thanks,

Steve