[Bioc-devel] Affy QA function for large chip set

[Ben Bolstad]

Not really a devel question, but in any case:

almost all the fitting functions in affyPLM (eg fitPLM(), threestep(),
etc) will take the argument background.method="GCRMA".

Then it is just a matter of applying the relevant QA function to the
output of the fitting function. However, I do not currently recommend
using the GCRMA background in combination with the NUSE(), RLE(),
image() QC tools.

Best,

Ben



On Fri, 2007-06-22 at 15:12 -0700, Ling, Ping [ALZUS] wrote:
> Hi Ben,
> 
> MAplot with plot.method = "smoothScatter" saves a small footprint in PDF file, and rendering of plot is fast. I also likes the type argument which controls the plot of pm, mm or both.
> 
> Another question,
> 
> In the AffyPLM package, many QA graphs are bi-products of RMA model fitting. If I like to see the same type of QA graphs for gcRMA model fitting, is there any way to go?
> 
> Thanks,
> 
> Ping
> 
> 
> 
> 
> -----Original Message-----
> From: Ben Bolstad [mailto:bmb at bmbolstad.com]
> Sent: Friday, June 22, 2007 6:14 AM
> To: Ling, Ping [ALZUS]
> Cc: bioc-devel at stat.math.ethz.ch
> Subject: Re: [Bioc-devel] Affy QA function for large chip set
> 
> 
> 
> > #3. ma.plot function in the affy package is pretty slow with probe level data, it renders a lot of data points in the output. When we come to export 100 MA plots with 6 MA plots per page in a PDF file, the file gets really big and navigation between pages becomes difficult.   I used a local weighted data point reduction sampling method to keep the contour and density profile of the MA plot while significantly reduce the data points. (I used such a method to retain similiar visual perspective with 5% data points).
> 
> you might want to consider using the "smoothScatter" plotting method,
> rather than just letting it plot all points with probe level data. This
> and other potential options for MAplot (which typically wraps ma.plot)
> are described here (though were it says exprSet, it should really say
> ExpressionSet):
> 
> http://bioconductor.org/packages/bioc/vignettes/affyPLM/inst/doc/MAplots.pdf
>