On Wed, Oct 17, 2012 at 8:06 AM, Jeremy Ng <jeremy.ng.wk1990@gmail.com>wrote:

> Hi List,
>
> I'm pretty new to R and BioConductor, but am trying to use Affy to process
> my CEL files for analysis.
>
> I understand the first step to doing this is to do an RMA normalization.
> Further, I used the ram argument in Affy to to an RMA normalization.
> however, the following error message gets returned:
>
> "Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain HuEx-1_0-st-v2
> Library - package huex10stv2cdf not installed
> Bioconductor - huex10stv2cdf not available"
>
>
Hi, Jeremy.

It looks like you are trying to work with HuEx arrays.  Take a look here:

http://www.bioconductor.org/help/workflows/oligo-arrays/#pre-processing-resources

In particular, you will probably want to use the oligo package (or another
on that list).  The affy package is for 3' pm/mm arrays.

Hope that helps.

Sean


The codes I used are as follows, after setting my working directory to the
> location of my CEL files:
> >library(affy)
> >c<- read.Affy()
>
> Once my CEL files (4 of them) have been read in, I attempted to run the RMA
> by invoking:
> >r<- rma(c, verbose=TRUE, normalization=TRUE, background=TRUE).
>
> Invoking this lead to the error message concerning the CDF environment
> issue. May I inquire as to how I can go about rectifying this?
>
> This is my session info:
> R version 2.15.1 (2012-06-22)
> 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
> [7] base
>
> other attached packages:
> [1] affy_1.36.0        Biobase_2.18.0     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] BiocInstaller_1.8.2   affyio_1.26.0         preprocessCore_1.20.0
> [4] tools_2.15.1          zlibbioc_1.4.0
>
> May I also ask for some suggestions on what kind of workflow should I
> follow? I'm interested in annotating alternative splicing events.
>
> Thanks a ton in advance!
>
> Jeremy
>
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