Following Steffen Durinck suggestion i am tying to annotate my anopheles afffyids with biomaRt and the functions of affycoretools (created by James MacDonald to make our life easy). After several attempts, I was able to get an almost working code but (I believe) the option fldfilt that allows a fold change cutoff is not working. I was wondering if the functions is not recognizing the M column because topTable (from limma package) change the columname M to "logFC" but I could not check this. best, Mayte limma2biomaRt (resetf,ebfit,designf,contr,species="agambiae",pfilt=0.001,fldfilt=log 2( 2),ann.source="affy_plasmodium_anopheles",links=linksBM() [1],interactive=FALSE,affyid=TRUE) connected to: ensembl Reading database configuration of: agambiae_gene_ensembl Checking main tables ... ok Checking attributes and filters ... ok Error in `[.data.frame`(tab, , "M") : undefined columns selected In addition: Warning message: NAs introduced by coercion limma2biomaRt (resetf,ebfit,designf,contr,species="agambiae",pfilt=0.001,ann.source= "a ffy_plasmodium_anopheles",links=linksBM() [1],interactive=FALSE,affyid=TRUE) connected to: ensembl Reading database configuration of: agambiae_gene_ensembl Checking main tables ... ok Checking attributes and filters ... ok Warning message: NAs introduced by coercion

Hi Mayte, Mayte Suarez-Farinas wrote: > Following Steffen Durinck suggestion i am tying to annotate my > anopheles afffyids with biomaRt and the functions of affycoretools > (created by James MacDonald > to make our life easy). > After several attempts, I was able to get an almost working code but > (I believe) the option fldfilt that allows a fold change cutoff is > not working. > I was wondering if the functions is not recognizing the M column > because topTable (from limma package) change the columname M to "logFC" > but I could not check this. I think you are correct, but this is likely due to mis-matched versions of limma and affycoretools. The release versions of these packages both use 'M' for the fold change, and the devel versions both use 'logFC', so you either need to go back to the release version of limma, or upgrade to R-2.5.0beta and use devel versions. Since we are releasing very soon, you might as well upgrade. Best, Jim > > best, > Mayte > > limma2biomaRt > (resetf,ebfit,designf,contr,species="agambiae",pfilt=0.001,fldfilt=l og2( > 2),ann.source="affy_plasmodium_anopheles",links=linksBM() > [1],interactive=FALSE,affyid=TRUE) > connected to: ensembl > Reading database configuration of: agambiae_gene_ensembl > Checking main tables ... ok > Checking attributes and filters ... ok > Error in `[.data.frame`(tab, , "M") : undefined columns selected > In addition: Warning message: > NAs introduced by coercion > > > limma2biomaRt > (resetf,ebfit,designf,contr,species="agambiae",pfilt=0.001,ann.sourc e="a > ffy_plasmodium_anopheles",links=linksBM() > [1],interactive=FALSE,affyid=TRUE) > connected to: ensembl > Reading database configuration of: agambiae_gene_ensembl > Checking main tables ... ok > Checking attributes and filters ... ok > Warning message: > NAs introduced by coercion > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.