Jim,

thanks for your reply, I think I have found these cdf and probe files and will have a go at creating custom packages using makecdfenv. 

cheers

nick


Dr Nick Wong BSc(Hons), Ph.D 
Postdoctoral Fellow
Cancer and Disease Epigenetics, Early Development and Disease 
 
Murdoch Childrens Research Institute 
The Royal Children’s Hospital 
Flemington Road Parkville Victoria 3052 Australia 
T 9936 6621 F 9348 1391 
M 0421 030 482 
E nick.wong@mcri.edu.au 
www.mcri.edu.au 



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On 09/12/2011, at 1:21 AM, James W. MacDonald wrote:

> Hi Nicholas,
> 
> On 12/5/2011 10:39 PM, Nicholas Wong wrote:
>> 
>> Hi all, first time poster long time reader.
>> 
>> I am trying to download and reanalyse publicly available gene expression sets that have used the custom U133A arrays that require the gnGNF1a library.
>> 
>> I have attached the error message and sessionInfo() below, but it would seem one can not install these libraries into the R 2.13.1, I have tried sourcing the library from a website and installing manually and the error as you can see is that it is not a valid installed package.
>> 
>> I think I would need to install an older version of R to accommodate for this, does anyone know what version this is? 
> 
> It's not an issue of the R version; instead it is an issue with that particular chip. We (meaning BioC) only create cdf and probe packages for Affy chips for which we can get the underlying data directly from Affymetrix. This necessarily excludes all custom chips, as Affymetrix have never to my knowledge made any custom chip data available.
> 
> The researchers who originally ran those chips may still have the cdf and probe data files, and may be willing to give them to you. If so, you can create your own cdf and probe packages using the makecdfenv and AnnotationDbi packages, respectively.
> 
> Best,
> 
> Jim
> 
> 
>> 
>> cheers
>> 
>> nick
>> 
>> 
>>> expData <- ReadAffy()
>>> expData
>> AffyBatch object
>> size of arrays=712x712 features (19 kb)
>> cdf=gnGNF1Ba (??? affyids)
>> number of samples=8
>> Error in function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
>>   'gngnf1bacdf' is not a valid installed package
>> In addition: Warning message:
>> missing cdf environment! in show(AffyBatch) 
>>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] C/en_US.UTF-8/C/C/C/C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>> 
>> other attached packages:
>> [1] affy_1.30.0    Biobase_2.12.2
>> 
>> loaded via a namespace (and not attached):
>> [1] affyio_1.20.0         preprocessCore_1.14.0 tools_2.13.1         
>> 
>> 
>> 
>> Dr Nick Wong BSc(Hons), Ph.D 
>> Postdoctoral Fellow
>> Cancer and Disease Epigenetics, Early Development and Disease 
>>  
>> Murdoch Childrens Research Institute 
>> The Royal Childrenâ€™s Hospital 
>> Flemington Road Parkville Victoria 3052 Australia 
>> T 9936 6621 F 9348 1391 
>> M 0421 030 482 
>> E nick.wong@mcri.edu.au 
>> www.mcri.edu.au 
>> 
>> 
>> 
>> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. 
>> 
>> ï Please consider the environment before printing this email 
>> 
>> 
>> 
>> 
>> 
>> 
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> -- 
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