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"

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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