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Question: warnings with affy package
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15.4 years ago by
Phguardiol@aol.com720 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 >
modified 15.4 years ago by Rafael A. Irizarry2.3k • written 15.4 years ago by Phguardiol@aol.com720
0
15.4 years ago by
Rafael A. Irizarry2.3k wrote:
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@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@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >