[BioC] scripted svg - was: Error using arrayQuality and Agilent txt files

[Wolfgang Huber]

Hi all

on a related note: the arrayQualityMetrics is since recently (currently 
only in the devel version) exploring ideas on how to make R-produced 
plots more interactive, using scripted svg, see e.g.
http://www-huber.embl.de/users/whuber/arrayQualityMetrics-Reports/MLL/QMreport.html 
Figs. 4, 6 and 8.

	Best wishes
	Wolfgang


Valerie Obenchain scripsit 12/10/10 18:51:
>
> 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 You are using an out of date version of R and Bioconductor.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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>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber