[BioC] Regarding Agi4x44PreProcess

[Tobias Straub]

hi sikha

apparently read.AgilentFE has to read information that is only written  
in a FULL feature table format export (which comprises e.g. chr_coord  
and sequence) in FE 10.5. most likely you did only COMPACT output (the  
default).

did you check the FULL option when doing the extraction?

best
tobias

On Aug 19, 2009, at 10:15 AM, shikha sinha wrote:

> Hi,
>
> Yes, I can use readmaimages in  limma but I feel using  
> Agi4x44PreProcess will make my work easier. I have used read.targets  
> for reading my target file and then read.AgilentFE for reading my  
> text raw data files. Please find below the commands I used and error  
> message I got:
>
> > targets=read.targets(infile="targets.txt")
>
> Target File
>                                                                                FileName 
>  treatment GErep
> US83000164_251485040272_S01_GE1_105_Dec08_1_1  
> US83000164_251485040272_S01_GE1_105_Dec08_1_1.txt         a     1
> US83000164_251485040272_S01_GE1_105_Dec08_1_2  
> US83000164_251485040272_S01_GE1_105_Dec08_1_2.txt         b     2
>
> > dd=read.AgilentFE(targets,makePLOT=FALSE)
> Read US83000164_251485040272_S01_GE1_105_Dec08_1_1.txt
> Read US83000164_251485040272_S01_GE1_105_Dec08_1_2.txt
> INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord
> SCANN THE DATA USING AFE 9.5.3.1
> Error in read.AgilentFE(targets, makePLOT = FALSE) :
>   the script will stop now
>
> Thanks & Regards
> Sikha
>
> --- On Wed, 19/8/09, Tobias Straub <tstraub at med.uni-muenchen.de>  
> wrote:
>
> From: Tobias Straub <tstraub at med.uni-muenchen.de>
> Subject: Re: [BioC] Regarding Agi4x44PreProcess
> To: "shikha sinha" <shikhakk2002 at yahoo.co.in>
> Cc: bioconductor at stat.math.ethz.ch
> Date: Wednesday, 19 August, 2009, 12:38 PM
>
> Hi Sikha,
>
> posting the command that caused the error and also the error message  
> would be helpful. In addition the output of sessionInfo() could help  
> to identify problems with potentially outdated versions of your R  
> packages.
>
> afaik Agi4x44PreProcess calls the read.maimages function of the  
> limma package to read the files. could you test if  
> read.maimages(filename, source="agilent) works for you?
>
> best
> Tobias
>
> On Aug 19, 2009, at 6:09 AM, shikha sinha wrote:
>
> > Hi,
> >
> > I am using Agi4x44PreProcess for preprocessing my agilent  
> microarray data. I have extracted data using Feature Extraction  
> v10.5. So, Agi4x44PreProcess is unable to read my raw data, But in  
> Help Pdf it has been written there that we can use it for FE 9.5 and  
> later on versions of FE.
> >
> > Please Help me
> >
> > Thanks,
> > Sikha
> >
> >
> >
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> ----------------------------------------------------------------------
> Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D
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Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D