[BioC] Error using arrayQuality and Agilent txt files

[Valerie Obenchain]

Clarification my message below :

The arrayQuality package should have the functionality you are looking
for ...
       ^^^^^^^^^^^^^^^

should have read


The arrayQualityMetrics package should have the functionality you are
looking for ...
        ^^^^^^^^^^^^^^^^^^^^^^^^


Valerie



On 10/12/2010 09:41 AM, Valerie Obenchain wrote:
> 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 You are using an out of date version of R and Bioconductor.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]]
>>
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>>     
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