Hi Charles' you've probably already noticed our Barley SFP paper and here is
the link to the method and data.  http://naturalvariation.org/barley .  In
this paper I first account for gene expression across all probes in a probe
set, the residuals are then fit probe wise for SFPs.  I didn't notice you
doing this in your code. Let me know if you can't navigate the supplement
script linked "barleySFP.R
<http://naturalsystems.uchicago.edu/naturalvariation/barley/barleySFP.R> "
see RNA section.. Good luck

Justin

 

 

Message: 5

Date: Sat, 6 May 2006 15:22:00 -0700

From: "Charles C. Berry" <cberry@tajo.ucsd.edu>

Subject: Re: [BioC] Communicating gene-probe relationships to sam

To: Charles Crane <ccrane@purdue.edu>

Cc: bioconductor@stat.math.ethz.ch

Message-ID: <Pine.LNX.4.64.0605061440310.27142@tajo.ucsd.edu>

Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

 

 

 

Charles,

 

You used method='cat.stat', which is (only) suitable for SNPs, I think.

 

This seems like an odd choice for detecting SFPs. You would have to do more
work to get this to work properly if you actually were counting SNPs

- i.e. you would have to **call** the SNPs. (And reasonably enough, sam()
doesn't like small sample numbers either.)

 

I suggest you use a linear model (method='d.stat') like the one in our
Genome Research paper available here:

 

      http://naturalsystems.uchicago.edu/naturalvariation/sfp/

 

BTW, sam() will not object to very small sample numbers with
'method="d.stat"'

 

HTH,

 

Chuck Berry

 

On Fri, 5 May 2006, Charles Crane wrote:

 

> Dear newsgroup:

>    I am trying to use sam to identify single-feature polymorphisms 

> between two barley cultivars.  I am running Bioconductor 1.7, Biobase 

> 1.8.0, affy 1.8.1, and siggenes 1.4.0 under Mac OS X 10.3.9.  I can 

> successfully extract probe-level data from my CEL files, background 

> correct the pm values with rma, quantile normalize, and isolate the pm 

> intensities in a data frame, but both sam and sam.snp consistently and 

> instantly fail with "Error in FUN(data, cl, ...) : There should be at 

> least 25 samples."  This happens even though there are 22840 genes and 

> 11 probes per gene in the data.  What am I overlooking?  Does sam need 

> some sort of a mapping from the 11 probes to their parent gene?  A session
history follows.

>    Thank your very much for your time.  Also, do you plan to include 

> directions for using sam for SNP analysis, going all the way from 

> ReadAffy through sam for a case history, in a future vignette?  It 

> would save the uninitiated a lot of time and frustration.

> 

> Charles Crane

> USDA-ARS, MWA, Crop Production and Pest Control Research Unit And 

> Department of Botany and Plant Pathology, Purdue University

 


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