[BioC] MEEBO-tool in arrayQuality

[Paquet, Agnes]

Hi Anja,

It looks like meeboQuality couldn't find  the controls identifiers. This function is looking for MEEBO ids starting with mMC, mCT, mCP...
Does your image processing output file include them? If so, did you try to specify the name of your column containing the MEEBO identifier in the arguments of the function?

Regards,

Agnes

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Anja Schiel
Sent: Fri 3/31/2006 4:51 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] MEEBO-tool in arrayQuality
 
Hello,
I am running the newest version of arrayQuality (1.6.3) to analyse MEEBO
arrays. We have spotted the library on two slides and I would like to
use the very nice new meebo-tool from the package. I get as far as
making the diagnostic plot, but seem to be unable to use the mismatch
controls or get the plots with the spike in ratios (I have adapted the
Spike in file, I only used Ambion Spikes).
This is my session output, in R 2.2.0, Linux, package 1.6.3.
Can anybody give me a hint what seems to go wrong with the NA at the
end?

 test<-meeboQuality(SpikeTypeFile="AmbionA.txt",
cy3col="MassCY3",cy5col="MassCY5", namecol="Name")
[1] "Staring meeboQuality"
Read ./AS240605_1.gpr
[1] "Starting meeboQualityPlots"
[1] TRUE
[1] TRUE
[1] TRUE
save as diagPlot.AS240605_1.png
Error: subscript out of bounds
Error in plot(as.numeric(ctl[mma, "NumberMM"]) * 100/70, mnorm
$A[as.vector(ctl[mma,  :
        unable to find the argument 'y' in selecting a method for
function 'NA'
>

Thanks, Anja


A. Schiel, Ph.D.
Department of Human Genetics
Leiden University Medical Center
Room T-03-054 
phone: 071 - 526 9472 
fax: 071 - 526 8275 
visiting address: 
Einthovenweg 20, Leiden 
postal address: 
LUMC 
Post zone S-4-P
PO Box 9600 
2300 RC Leiden 



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