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Phguardiol@aol.com
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720
@phguardiolaolcom-152
Last seen 9.6 years ago
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
>
