[BioC] SimpleAffy qc problem

[James W. MacDonald]

Hi Daofeng,

Daofeng Li wrote:
> Could someone give some help or suggestion?

You could search the BioC list. IIRC, somebody posted a function to add 
your own qc parameters to simpleaffy.

Best,

Jim


> Thanks in advance:)
> 
> Li
> 
> 
> On 6/5/07, Daofeng Li <lidaof at gmail.com> wrote:
> 
>>my sessioninfo:
>>
>>>sessionInfo()
>>
>>R version 2.5.0 (2007-04-23)
>>i686-pc-linux-gnu
>>
>>locale:
>>LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>>
>>attached base packages:
>>[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
>>[7] "datasets"  "methods"   "base"
>>
>>other attached packages:
>>medicagocdf  simpleaffy  genefilter    survival        affy      affyio
>>   "1.16.0"    "2.10.3"    "1.14.1"      "2.31"    "1.14.0"     " 1.4.0"
>>    Biobase
>>   "1.14.0"
>>
>>
>>On 6/5/07, Daofeng Li <lidaof at gmail.com> wrote:
>>
>>>Hi all,
>>>
>>>i am use R 2.5.0 and BioC 2.0 under a CentOS 4.4 server
>>>i am doing a Medicago Genechip
>>>when i do the qc function provided by simpleaffy
>>>it says
>>> "
>>>
>>>>qc <- qc(raw.data, x.mas )
>>>
>>>Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
>>>chip type: medicagocdf
>>>"
>>>i searched with Google,find no solution
>>>is there some idea about that now?
>>>
>>>Thanks!
>>>--
>>>Daofeng Li
>>
>>
>>
>>
>>--
>>Daofeng Li
> 
> 
> 
> 
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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