[BioC] Error using arrayQuality and Agilent txt files

[Valerie Obenchain]

Hi Javier,

You are using an out of date version of R and Bioconductor. You should
update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC
2.7 will be available.
http://www.bioconductor.org/install/index.html

I would suggest using the arrayQualityMetrics package instead of
arrayQuality.  The arrayQuality package should have the functionality
you are looking for along with helpful documentation and active maintainers.
Let me know if you have problems.

Valerie



On 10/08/2010 05:24 AM, F. Javier López wrote:
>   Dear All,
>
>   I am trying to use the arrayQuality package with a set of two-color
> Agilent arrays (G2519F AMADID 014868 MOUSE 4x44), but I am just getting an
> error which I do not know how to overcome. Some details of the attempts we
> made:
>
>   R version: 2.10.1 (also tried on 2.7.0)
>   Packages version: arrayQuality_1.24.0, limma_3.2.3, RColorBrewer_1.0-2,
> gridBase_0.4-3, hexbin_1.22.0, lattice_0.18-3, convert_1.22.0,
> Biobase_2.6.1, marray_1.24.0
>   Raw data format: txt files obtained with the "Feature Extraction" Agilent
> software (You can have a look at the file header here:
> http://bioinformatics.fcrb.es/documentacion/header.txt).
>
>   We first tried to use the agQuality function:
>
>   
>> agQuality("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt")
>>     
> [1] "Starting agQuality..."
> Reading ...  ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt
> Error in slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) :
>   dims [product 45018] do not match the length of object [0]
>
>   It seemed that there were some kind of problem with file format, so we
> tried to do it by reading with read.maimages and then using maQualityPlots:
>
>   
>>     
> RG<-read.maimages("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt","agilent",columns
> = list(G = "gMedianSignal",Gb = "gBGMedianSignal",R
> ="rMedianSignal",Rb="rBGMedianSignal"),other.columns=c("gIsPosAndSignif","rIsPosAndSignif"),annotation=
> c("Row","Col","ProbeUID","ProbeName","GeneName","accessions","SystematicName","ControlType"))
> # This text file corresponds to one of the four arrays in the slide
> Read US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt
>   
>> colnames(RG$genes)[2] <- "Column"
>> RG$genes$Block <- rep(1, length(RG$genes$ProbeName)) # There is only one
>>     
> block in the array
>   
>> RG$printer <- getLayout(RG$genes)
>> maQualityPlots(RG)
>>     
> Error: dims [product 45018] do not match the length of object [45220]
> In addition: Warning messages:
> 1: In samplesub & which :
>   longer object length is not a multiple of shorter object length
> 2: In samplesub & which & subset & good :
>   longer object length is not a multiple of shorter object length
>
>   It seems to be a problem with the array layout. There are only 45022
> rows(probes) in the txt file from which 45018 are read by read.maimage, but
> also, the maximum row and column coordinates of the spots are 532 and 85
> respectively. Multiplying 532x85 gives 45220, which is the expected size of
> the complete array. So, is it possible that the "Feature Extraction"
> software is filtering out some spots? Is it possible to run maQualityPlots
> if these spots are missing? Any clue?
>
>   Thank you very much.
>
>   Regards,
>
>   F. Javier Lopez
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>