[BioC] Tiling array application

[Kasper Daniel Hansen]

On Fri, Apr 01, 2005 at 08:04:28PM -0500, James MacDonald wrote:
> It doesn't make any sense to use gcrma() if you don't have MM probes;
> the idea behind gcrma is to come up with a better measure of background
> than the MM measure itself. A modification of gcrma() that doesn't use
> MM probes is rma().

And if you are using a tiling array it does not seem to make sense (to 
me at least) to use rma, since tiling arrays does not have the cpncept 
of probesets.

But I do not know your particular array, so I may be wrong.

Kasper

> >>> Shinhan Shiu <shiu at uchicago.edu> 04/01/05 5:13 PM >>>
> We are trying to use GCRMA to adjust raw intensity values from tiling
> chip 
> experiments (Arabidopsis). But the affy Arabidopsis tiling chip do not
> have 
> mismatch probes and it seems the mismatch probe intensity is absolutely 
> required in:
> 
> bg.parameters.ns
> 
> Where the mismatch probe intensities, mismatch probe affinity, and
> perfect 
> match probe affinities are passed. I wonder how this function can be 
> modified so only perfect match probe info is used. Thanks.
> 
> Shinhan
> 
> 
> ********************************
>   Shinhan Shiu
>   Dept. of Ecology and Evolution
>   University of Chicago
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> 
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

-- 
Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen