[BioC] frma for Nimblegen arrays?

[Hollis Wright]

Thanks, Matthew. As a followup, is there no longer an annotation package available for the rat arrays for oligo? I'm getting an error: 

biocLite("pd.100718.rat.hx12.expr")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'pd.100718.rat.hx12.expr'
Warning messages:
1: package ‘pd.100718.rat.hx12.expr’ is not available (for R version 2.15.0) 

I searched the Bioconductor site and the package doesn't come up, and I can't seem to find anything with Google either. Is this just a version thing? 

Hollis Wright, PhD
Ojeda Lab, Division of Neuroscience
Oregon Health and Science University


________________________________________
From: Matthew McCall [mccallm at gmail.com]
Sent: Monday, October 29, 2012 9:41 AM
To: Hollis Wright
Cc: bioconductor at r-project.org
Subject: Re: [BioC] frma for Nimblegen arrays?

Hollis,

1. I highly doubt that Nimblegen is using fRMA.

2. There isn't an fRMA implementation for Nimblegen arrays currently.
You could in theory use a modified version of the code in the
frmaTools package to make your own vectors, but it is probably better
to just use RMA.

Best,
Matt

On Mon, Oct 29, 2012 at 12:35 PM, Hollis Wright <wrighth at ohsu.edu> wrote:
> Hello, all: two-part question here. We have some expression data from Nimblegen rat arrays that was normalized from our microarray service using the internal RMA process Nimblegen uses in their software. Unfortunately, a few of the arrays had physical defects. We've pulled those from our downstream analysis just to be safe but we're unsure if they were used in the normalization process. We've gone ahead with downstream analysis but I'd also like to make sure we're not running into any issues that were baked into the current normalization, just to be safe. So:
>
> 1) Should we be concerned in the first place about whether or not these arrays were included in the normalization process? I can't seem to find out exactly what flavor of RMA variant Nimblegen is using. If it's frma, since the normalizations are precomputed it shouldn't matter if the bad arrays were included, should it?
>
> 2) Assuming we should be concerned and renormalize, is this easily possible with frma? We have non-normalized data but we don't have the tiff files, just the calls/pairs/xys files. Is that sufficient? Sorry for the basic questions, I've not done microarray normalization in quite a while and that was all on an Affy platform.
>
> Thanks!
>
> Hollis Wright, PhD
> Ojeda Lab, Division of Neuroscience
> Oregon Health and Science University
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