[BioC] Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"

[Sean Davis]

On Sun, Mar 23, 2008 at 2:58 PM, Suprabhath Reddy Gajjala
<sgajjala at emich.edu> wrote:
> Hello Everyone,
>
>  I am writing programs in R from 7 months and I am able to solve most of
>  the errors/issues except for this current post.
>
>  My Task is to read a Microsoft Excel file(textE_to_affy.csv) which
>  contains the Microarray Expression Values collected from the Illumina
>  Microarray experiment. These collected intensity values need to be
>  normalized(Rank Invariant Normalization) by using the R function
>  "normalize.AffyBatch.invariantset()".

Ilumina data are actually quite different in many respects from Affy
data.  You will be better off looking at the beadarray or lumi
packages.  In particular, in the beadarray package, you would use
readBeadSummaryData() followed by rankInvariantNormalise() to
accomplish the task you stated in your email.  Rank invariant
normalization has some drawbacks, the largest one, in my opinion,
being the generation of negative values.  Both the lumi and beadarray
packages have multiple other normalization methods available.

Sean