[BioC] maQualityPlots (arrayQuality package)

[Paquet, Agnes]

Dear Joao,
 
This problem is most likely due to the format of your control spots.  arrayQuality is looking for controls which are replicated more that 3 times on your array (more that 3 times the same oligo id). If you don't have such controls or if you didn't set up your controls properly in your RG object, maQualityPlots will fail. One way  to check if your array have such controls could be to use the example R code below:
 
test=table(RG$gene$Status)
controlId="ID" ## Use the column name from your gpr file containing oligo Ids if it's not ID
## For each type of control, check how many oligos are replicated,
## Return the number of ids replicated more than 3 times (and how many times they are replicated
for(i in c(1:length(test))[names(test)!="probes"])
  {
    print(i)
    print(table(RG$gene[RG$genes$Status == names(test)[i],controlId])[table(RG$gene[RG$genes$Status == names(test)[i],controlId])>3])
  }

If this code returns 'named integer(0)' only, then you don't have enough control replication. If it returns something else, or if you have any problem running this code, could you please send me the R output so that I can work more on this problem?
 
Best,
 
Agnes
  

________________________________

From: bioconductor-bounces at stat.math.ethz.ch on behalf of João Fadista
Sent: Mon 3/26/2007 5:09 AM
To: Sean Davis; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] maQualityPlots (arrayQuality package)



Dear Sean,

You are right. Here it is some back information:

> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"    

other attached packages:
     sma    limma
"0.5.15" "2.9.13"


> RG <- read.maimages(fnames, source="genepix.custom", path=datadir, ext="gpr", columns=columns, wt.fun=wtflags(weight=0,cutoff=0))

> RG$printer <- getLayout(RG$genes,guessdups=TRUE)   # extract the layout from the RG$printer

> types <- readSpotTypes("SpotTypes.txt",path=genedir)

> RG$genes$Status <- controlStatus(types, RG)

> library(arrayQuality)

> maQualityPlots(RG)
> [1] TRUE
> [1] TRUE
> [1] TRUE
> Error in exty[[i]] : subscript out of bounds

Note: My RG has 6 samples in it (3 replicates with dye swap each).


Best regards

João Fadista
Ph.d. student


UNIVERSITY OF AARHUS
Faculty of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
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DK-8830 Tjele

Phone:   +45 8999 1900
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E-mail:  Joao.Fadista at agrsci.dk
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-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
Sent: Monday, March 26, 2007 12:31 PM
To: bioconductor at stat.math.ethz.ch
Cc: João Fadista
Subject: Re: [BioC] maQualityPlots (arrayQuality package)

On Monday 26 March 2007 03:22, João Fadista wrote:
> Dear all,
>
> I found a problem with the function maQualityPlots from the
> arrayQuality
package. It outputs the following message:
> > maQualityPlots(RG)
>
> [1] TRUE
> [1] TRUE
> [1] TRUE
> Error in exty[[i]] : subscript out of bounds
>
> Does anybody knows what seems to be the problem? Thanks in advance.

Joao,

You will probably need to supply some more detail.  The best way to post questions like this is to supply all the commands in a reproducible example. 
Short of that, at least the commands to produce "RG" need to be present. 
Also, the output from sessionInfo() pretty much has to be in all questions to this list, considering the multiple versions of bioconductor packages and R and multiple operating systems.

Sean

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