Benilton,

Thank you so much for writing back. My apologies if I've come across very
negatively. I do realize documentation and development are ongoing
processes, and I have been incredibly impressed by the extensive docs
available for most Bioconductor packages.

The code sample is exactly the kind of thing I'm looking for. I'll spend
some time tomorrow playing around with it.


Aside from feedback, is there anything else I can do to help as I go through
this, such as writing a vignette? I've been experimenting with Sweave a bit.


Cheers,
John



On Wed, Jul 23, 2008 at 5:50 PM, Benilton Carvalho <bcarvalh@jhsph.edu>
wrote:

> Dear John,
>
> my apologies for not being very helpful, but the combo oligo+pdInfoBuilder
> is meant to help you with expression, SNP, tiling, exon and gene arrays.
>
> Because I've been working more closely with SNP arrays, the interface for
> SNPs is a bit more developed. And, slowly, I'm adding functionalities for
> other platforms.
>
> Soon I'll be able to give more attention to both packages, but you can get
> started by creating the pdInfo package for the array you have.
>
> The code I use to create such package is:
>
> library(pdInfoBuilder)
> bpmapFile <- "Hs_PromPR_v02-3_NCBIv36.bpmap"
> cifFile <- "Hs_PromPR_v02.cif"
> obj <- new("AffyTilingPDInfoPkgSeed",
>           version="0.0.1",
>           author="Benilton Carvalho", email="bcarvalh@jhsph.edu",
>           biocViews="AnnotationData",
>           genomebuild="NCBI Build 36",
>           bpmapFile=bpmapFile,
>           cifFile=cifFile)
> makePdInfoPackage(obj, destDir=".")
>
>
> And, after installing the resulting package, I'm able to read in the CEL
> files. As I said, there isn't much implemented specific for Tiling Arrays,
> and it would be actually very helpful to have feedback from "tiling arrays'
> users".
>
> Cheers,
>
> b
>
>

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