[BioC] agi4x44kpreprocess package

[Erika Melissari]

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!
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]]
>>
>> _______________________________________________
>> 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
>


--------------------------------------------------------------------------------



Nessun virus nel messaggio in arrivo.
Controllato da AVG - www.avg.com
Versione: 8.0.233 / Database dei virus: 270.10.17/1932 -  Data di rilascio: 
02/02/09 07:51:00