[BioC] Anopheles annotation using limma2biomaRt: error with fldfilt option

[James W. MacDonald]

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=log2( 
> 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
> 
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-- 
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


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