It sounds like that "summarize to the probe-level" is simply normalize the
data (possibly after background correction) and not summarize at all?

library(oligoData)
data(nimbleExpressionFS)
pns = probeNames(nimbleExpressionFS)
sns = sampleNames(nimbleExpressionFS)
pms = pm(nimbleExpressionFS)
pms = backgroundCorrect(pms)
pms = normalize(pms)
colnames(pms) = sns
rownames(pms) = pns
head(pms)


b


On 10 November 2012 00:02, Hollis Wright <wrighth@ohsu.edu> wrote:

> 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@gmail.com]
> Sent: Tuesday, October 30, 2012 10:38 AM
> To: Hollis Wright
> Cc: bioconductor@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@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@gmail.com]
> > Sent: Tuesday, October 30, 2012 2:56 AM
> > To: Hollis Wright
> > Cc: bioconductor@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@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@gmail.com]
> >> Sent: Monday, October 29, 2012 9:41 AM
> >> To: Hollis Wright
> >> Cc: bioconductor@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@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
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >>
> >> --
> >> Matthew N McCall, PhD
> >> 112 Arvine Heights
> >> Rochester, NY 14611
> >> Cell: 202-222-5880
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
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>

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