Of the various Bioconductor methods, is there any which performs a
fairly generic loess normalization, leaving out fancy stuff like
print-tip normalization, etc?
I'd like to write some code based on this, so I'd like to see a
stripped-down example if there is one out there.
Thanks.
Gene Cutler
Principal Scientist
Bioinformatics
Amgen SF
On Mar 2, 2005, at 9:09 PM, Gene Cutler wrote:
> Of the various Bioconductor methods, is there any which performs a
> fairly generic loess normalization, leaving out fancy stuff like
> print-tip normalization, etc?
>
> I'd like to write some code based on this, so I'd like to see a
> stripped-down example if there is one out there.
>
Limma has multiple methods for normalizationWithinArrays. See the
help
page for that function. Also, the marray package includes a (slower)
loess normalization.
Sean
Gene Cutler wrote:
> Of the various Bioconductor methods, is there any which performs a
> fairly generic loess normalization, leaving out fancy stuff like
> print-tip normalization, etc?
>
> I'd like to write some code based on this, so I'd like to see a
> stripped-down example if there is one out there.
You might look at loessFit in the limma package. Much of the heavy
lifting appears to be done in C, however.
Jim
>
> Thanks.
>
>
>
> Gene Cutler
> Principal Scientist
> Bioinformatics
> Amgen SF
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Hi Gene,
for general local regression, you may also want to look at the locfit
package (on CRAN) which one might call a faster and more advanced
version of loess. It provides better diagnostic output and there is a
very nice textbook going with it.
Best wishes
Wolfgang
James W. MacDonald wrote:
> Gene Cutler wrote:
>
>> Of the various Bioconductor methods, is there any which performs a
>> fairly generic loess normalization, leaving out fancy stuff like
>> print-tip normalization, etc?
>>
>> I'd like to write some code based on this, so I'd like to see a
>> stripped-down example if there is one out there.
>
>
> You might look at loessFit in the limma package. Much of the heavy
> lifting appears to be done in C, however.
>
> Jim
>
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax: +44 1223 494486
Http: www.ebi.ac.uk/huber
