[BioC] warnings with affy package

[Rafael A. Irizarry]

those warnings are returned by the function loess. in my experience the
final result seem to be what one expects so i ignore them. 

On Sat, 10 May 2003 Phguardiol at aol.com wrote:

> Hi
> I ve been running an analysis with the affy package and I am getting some warnings. I dont exactly know what to think about these...(see below)
> I m using a P4, winXP, 1G0 RAM with R1.7 and the development packages (the last one from today !)
> 
> R : Copyright 2003, The R Development Core Team
> Version 1.7.0  (2003-04-16)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type `license()' or `licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type `contributors()' for more information.
> 
> Type `demo()' for some demos, `help()' for on-line help, or
> `help.start()' for a HTML browser interface to help.
> Type `q()' to quit R.
> 
> > library(affy)
> *************
> affy: development version
> *************
> *************
> IMPORTANT: you need the latest versions of the required packages too.
> *************
> Welcome to Bioconductor 
>          Vignettes contain introductory material.  To view, 
>          simply type: openVignette() 
>          For details on reading vignettes, see
>          the openVignette help page.
> Creating a new generic function for "summary" in package 
> reposTools 
> 
> Synching your local package management information ...
> > data<-ReadAffy()
> > data2<-expresso(data, bgcorrect.method="rma", normalize.method="loess", pmcorrect.method="pmonly", summary.method="medianpolish")
> background correction: rma 
> normalization: loess 
> PM/MM correction : pmonly 
> expression values: medianpolish 
> background correcting...done.
> normalizing...Done with 1 vs 2  in iteration  1 
> Done with 1 vs 3  in iteration  1 
> Done with 1 vs 4  in iteration  1 
> Done with 1 vs 5  in iteration  1 
> Done with 1 vs 6  in iteration  1 
> Done with 1 vs 7  in iteration  1 
> Done with 1 vs 8  in iteration  1 
> Done with 2 vs 3  in iteration  1 
> Done with 2 vs 4  in iteration  1 
> Done with 2 vs 5  in iteration  1 
> Done with 2 vs 6  in iteration  1 
> Done with 2 vs 7  in iteration  1 
> Done with 2 vs 8  in iteration  1 
> Done with 3 vs 4  in iteration  1 
> Done with 3 vs 5  in iteration  1 
> Done with 3 vs 6  in iteration  1 
> Done with 3 vs 7  in iteration  1 
> Done with 3 vs 8  in iteration  1 
> Done with 4 vs 5  in iteration  1 
> Done with 4 vs 6  in iteration  1 
> Done with 4 vs 7  in iteration  1 
> Done with 4 vs 8  in iteration  1 
> Done with 5 vs 6  in iteration  1 
> Done with 5 vs 7  in iteration  1 
> Done with 5 vs 8  in iteration  1 
> Done with 6 vs 7  in iteration  1 
> Done with 6 vs 8  in iteration  1 
> Done with 7 vs 8  in iteration  1 
> 1 0.4074713 
> done.
> 22283 ids to be processed
> .........
> There were 21 warnings (use warnings() to see them)
> > warnings()
> Warning messages:
> 1: k-d tree limited by memory. ncmax= 5002
> 2: k-d tree limited by memory. ncmax= 5002
> 3: k-d tree limited by memory. ncmax= 5002
> 4: k-d tree limited by memory. ncmax= 5002
> 5: k-d tree limited by memory. ncmax= 5002
> 6: k-d tree limited by memory. ncmax= 5002
> 7: k-d tree limited by memory. ncmax= 5002
> 8: k-d tree limited by memory. ncmax= 5002
> 9: k-d tree limited by memory. ncmax= 5002
> 10: k-d tree limited by memory. ncmax= 5002
> 11: k-d tree limited by memory. ncmax= 5002
> 12: k-d tree limited by memory. ncmax= 5002
> 13: k-d tree limited by memory. ncmax= 5002
> 14: k-d tree limited by memory. ncmax= 5002
> 15: k-d tree limited by memory. ncmax= 5002
> 16: k-d tree limited by memory. ncmax= 5002
> 17: k-d tree limited by memory. ncmax= 5002
> 18: k-d tree limited by memory. ncmax= 5002
> 19: k-d tree limited by memory. ncmax= 5002
> 20: k-d tree limited by memory. ncmax= 5002
> 21: k-d tree limited by memory. ncmax= 5002
> >
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>