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

[Mayte Suarez-Farinas]

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=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