[BioC] warnings with affy package

Phguardiol at aol.com Phguardiol at aol.com
Sat May 10 21:13:28 MEST 2003


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 !)

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> 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
>



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