[BioC] Agi4x44Preprocess - error on read.AgilentFE fucntion

[James W. MacDonald]

Hi Amanda,

On 1/23/2014 12:04 PM, Amanda F A Riccardi [guest] wrote:
> Hello everybody!
>
> I'm using Agi4x44Preprocess package to deal with pre processing Agilent single color 4x44 whole mouse genome array, which data were obtained using feature extraction software.
>   The problem is that I can't download my data with the function read.AgilentFE, I got an error - showed below - and the script just stop and, instead mine,  the author's example data is imported... I used read.maimages function of the package limma as an alternative, but I really would like to know what is wrong using read.AglentFE.
> Regards,
> Amanda
>
>   -- output of sessionInfo():
>
>> targets <- read.targets(infile="targets.txt")
>   
> Target File
>       FileName Treatment Gerep
> CT1  CT1.txt        CT     1
> CT2  CT2.txt        CT     1
> CT3  CT3.txt        CT     1
> TT1  TT1.txt        TT     2
> TT2  TT2.txt        TT     2
> TT3  TT3.txt        TT     2
> PT1  PT1.txt        PT     3
> PT2  PT2.txt        PT     3
> PT3  PT3.txt        PT     3
>
>> dd <-read.AgilentFE(targets,makePLOT=TRUE)
> Read CT1.txt
> Read CT2.txt
> Read CT3.txt
> Read TT1.txt
> Read TT2.txt
> Read TT3.txt
> Read PT1.txt
> Read PT2.txt
> Read PT3.txt
>   INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord
>   SCANN THE DATA USING AFE 9.5.3.1

^^^^^^^^^ That is supposed to be your hint. What it means is that the 
sequence and chromosome coordinate data are not available, and that you 
should use Agilent Feature Extraction version 9.5.3.1 (or higher, I 
presume).

If you don't have these data available, read.AgilentFE() will fail, as 
this test is hard-coded into the function. In other words, unless you 
upgrade your AFE version, you will have to use read.maimages() directly.

Best,

Jim


> Erro em read.AgilentFE(targets, makePLOT = TRUE) :
>     the script will stop now
>    
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099