[BioC] agi4x44kpreprocess package

Francois Pepin fpepin at cs.mcgill.ca
Wed Feb 4 02:01:24 CET 2009 

Hi Pedro,

Out of curiosity, is there anything specific to 4x44k arrays in the 
package, as opposed to 1x44k or 244k arrays?

If not, it might be worth considering renaming the package to something 
a bit more general, like AgiPreProcess or AgiOneColorPreProcess.

Francois

Pedro López Romero wrote:
> Hi everyone, 
>  
> Sean is right. Agilent advocates now for the use of one-single color arrays and we have designed Agi4x44PreProcess for the analysis of this sort of data. To get the data into R, we use the limma function read.maimages, but we only get the green signals since these are the only signals that we have in our data files. 
>  
> To be more precise, the function read.AgilentFE uses the limma function read.maimages that creates an RGList object, for example:
>  
> dd=read.AgilentFE(targets,makePLOT=FALSE)
>  
> dd is the RGList  that includes
>  
>    dd$Rf="gProcessedSignal",
>    dd$Gf="gMeanSignal",
>    dd$Rb="gBGMedianSignal",
>    dd$Gb="gBGUsed"
>  
> all of which are green signals. Depending on how you want to process your data you might select one or another signal from the ones provided according to different methods of backround correction. 
>  
> The package cannot be used for the processing of two-single color arrays. 
>  
> HTH
>  
> Pedro 
> 
> ________________________________
> 
> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Sean Davis
> Sent: Tue 2/3/2009 5:33 PM
> To: Erika Melissari
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] agi4x44kpreprocess package
> 
> 
> 
> On Tue, Feb 3, 2009 at 10:54 AM, Erika Melissari <
> erika.melissari at bioclinica.unipi.it> wrote:
> 
>> Hello Francois,
>>
>> thank you for your help.
>>
>> here is the sessionInfo() output
>>
>> R version 2.8.0 (2008-10-20)
>> 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] splines   tools     stats     graphics  grDevices utils     datasets
>> methods
>> [9] base
>>
>> other attached packages:
>> [1] hgug4112a.db_2.2.5      RSQLite_0.7-1           DBI_0.2-4
>> [4] Agi4x44PreProcess_1.2.0 genefilter_1.22.0       survival_2.34-1
>> [7] annotate_1.20.1         xtable_1.5-4            AnnotationDbi_1.4.1
>> [10] limma_2.16.3            Biobase_2.2.1
>>
>> I realized that this package is wrapped around limma, but the result of
>> read.maimages is not the same.
>> I have checked, comparing the loaded data with raw data, what date have
>> been loaded by using read.AgilentFe of agi4x44preprocess and, really, only
>> the green signals are loaded. Obviously, the read.maimages() load the
>> correct data (I have checked).
>> The problem is that agi4x44preprocess vignette also affirm that the signals
>> loaded are the green signals...but I do not understand why only green!
> 
> 
> For gene expression arrays, Agilent has been advocating single-channel
> protocols for a couple of years.  There are groups for which that is the
> standard.
> 
> Sean
> 
> 
> 
>> I am evaluating this package because it offer some functions for managing
>> the huge amount of data (processed signals, mean signals and, above all, the
>> flags) extracted by using Feature extraction software by Agilent. I would
>> like to use the complicated system of Agilent flags for quality control of
>> my microarray data and only this package manages to do this.
>> Thank you for any suggestion.
>>
>> Erika
>>
>> ----- Original Message ----- From: "Francois Pepin" <fpepin at cs.mcgill.ca>
>> To: "Erika Melissari" <erika.melissari at bioclinica.unipi.it>
>> Cc: <bioconductor at stat.math.ethz.ch>
>> Sent: Tuesday, February 03, 2009 16:20 PM
>> Subject: Re: [BioC] agi4x44kpreprocess package
>>
>>
>>  Hi Erika,
>>> I have never used that package, but it seems to be mostly a wrapper
>>> around limma for those steps. What happens if you use
>>> read.maimages(files, source='agilent') directly?
>>>
>>> You might also want to make sure that you have red values if you look
>>> directly in your raw text file.
>>>
>>> And please post the output from sessionInfo(). This will make it easier
>>> for people to understand which type of installation you have, and
>>> generally makes it easier to catch if the problem.
>>>
>>> Francois
>>>
>>> Erika Melissari wrote:
>>>
>>>> Hello all,
>>>>
>>>> does anyone know Agi4x44kPreProcess package?
>>>> I'm exploring it to perform pre-process steps on human 4x44k Agilent
>>>> microarrays, but I have a question or perhaps a doubt: why does this package
>>>> load only the green signals (processed, mean, ect.) and not the red signals?
>>>> Is it an error of this package or a characteristic?
>>>> Thank you so much for any indication
>>>>
>>>> Erika
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
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>>>
>>
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