[BioC] frma for Nimblegen arrays?

[Hollis Wright]

Quick (belated) followup question on this: is it possible to get oligo to summarize the probe-level expression rather than the gene level expression? We'd like to try to experiment with some of the other gene-level methods (such as the WGCNA collapseRows, for example) and just see how individual probes may be doing. I tried using the target="probeset" argument and that doesn't seem to work. Would I need to specify something when I set up the annotation object from the NDF? 

Hollis Wright, PhD
Ojeda Lab, Division of Neuroscience
Oregon Health and Science University
________________________________________
From: Benilton Carvalho [beniltoncarvalho at gmail.com]
Sent: Tuesday, October 30, 2012 10:38 AM
To: Hollis Wright
Cc: bioconductor at r-project.org
Subject: Re: [BioC] frma for Nimblegen arrays?

The "generic XYS file" is meant to be actually one of your samples
(any of them, its just to work as a template)... So, I'm confident you
did everything right. b :)

On 30 October 2012 16:58, Hollis Wright <wrighth at ohsu.edu> wrote:
> Thanks, Benilton; I think I figured it out with buildPDInfoPkgs. However, just to be sure; we were provided an NDF file but I don't think we got a generic XYS file, so I used one of the actual array files for the XYS. It seemed to work alright, but could that be problematic?
>
> Hollis Wright, PhD
> Ojeda Lab, Division of Neuroscience
> Oregon Health and Science University
>
> ________________________________________
> From: Benilton Carvalho [beniltoncarvalho at gmail.com]
> Sent: Tuesday, October 30, 2012 2:56 AM
> To: Hollis Wright
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] frma for Nimblegen arrays?
>
> Hi Hollis,
>
> I'm the one who builds all the annotation packages for and I'm
> positive that this annotation package was never provided through
> BioC... I'm happy to help you out with that though.
>
> benilton
>
> On 29 October 2012 18:17, Hollis Wright <wrighth at ohsu.edu> wrote:
>> 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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>>
>>
>>
>> --
>> Matthew N McCall, PhD
>> 112 Arvine Heights
>> Rochester, NY 14611
>> Cell: 202-222-5880
>>
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