Question: how to install gnGNF1a cdf and probe files to a recent version of R (2.13.1)?
6.0 years ago by
Nicholas Wong • 30
Nicholas Wong • 30 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? 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:  C/en_US.UTF-8/C/C/C/C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  affy_1.30.0 Biobase_2.12.2 loaded via a namespace (and not attached):  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 Childrenâs Hospital Flemington Road Parkville Victoria 3052 Australia T 9936 6621 F 9348 1391 M 0421 030 482 E email@example.com 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 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ [[alternative HTML version deleted]]
ADD COMMENT • link •