[BioC] maQualityPlots (arrayQuality package)

[João Fadista]

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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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