Hi,

I noticed a problem with biomart driven ensembl querys and it seems that the behaviour depends on the ensembl version used. I'm trying to obtain ggallus homologs for mouse genes on all autosomes and the X. With the May 2015 ensembl archive I need to query each chromosome in a loop to prevent missing genes, with the March 2015 version I can query all chromosomes at once.

library(biomaRt)
ensembl.new <- useMart("ENSEMBL_MART_ENSEMBL",host="may2015.archive.ensembl.org")
ensemblmmusculus.new = useDataset("mmusculus_gene_ensembl",mart=ensembl.new)
aa <- lapply(c("X",as.character(1:19)),function(x) getBM(attributes = c("ensembl_gene_id", "ggallus_homolog_orthology_type", "ggallus_homolog_orthology_confidence","ggallus_homolog_chromosome", "chromosome_name"), filter="chromosome_name", values=x, mart=ensemblmmusculus.new))
print(Reduce("+",lapply(aa,nrow)))
chromosome.input <- getBM(attributes = c("ensembl_gene_id", "ggallus_homolog_orthology_type", "ggallus_homolog_orthology_confidence","ggallus_homolog_chromosome", "chromosome_name"), filter="chromosome_name", values=c("X",as.character(1:19)), mart=ensemblmmusculus.new)
print(nrow(chromosome.input))

ensembl.new <- useMart("ENSEMBL_MART_ENSEMBL",host="mar2015.archive.ensembl.org")
ensemblmmusculus.new = useDataset("mmusculus_gene_ensembl",mart=ensembl.new)
aa <- lapply(c("X",as.character(1:19)),function(x) getBM(attributes = c("ensembl_gene_id", "ggallus_homolog_orthology_type", "ggallus_homolog_orthology_confidence","ggallus_homolog_chromosome", "chromosome_name"), filter="chromosome_name", values=x, mart=ensemblmmusculus.new))
print(Reduce("+",lapply(aa,nrow)))
chromosome.input <- getBM(attributes = c("ensembl_gene_id", "ggallus_homolog_orthology_type", "ggallus_homolog_orthology_confidence","ggallus_homolog_chromosome", "chromosome_name"), filter="chromosome_name", values=c("X",as.character(1:19)), mart=ensemblmmusculus.new)
print(nrow(chromosome.input))

The difference can be clearly seen in the number of rows the print results show. For the May version I get 44679 genes for the loop and 27372 for the non-looped version. With the March version I get 42561 genes for both ways.

sessionInfo()

R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 7 (wheezy)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=C            
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.24.0

loaded via a namespace (and not attached):
 [1] compiler_3.2.1       IRanges_2.0.1        DBI_0.3.1           
 [4] parallel_3.2.1       tools_3.2.1          RCurl_1.95-4.6      
 [7] Biobase_2.26.0       AnnotationDbi_1.30.1 RSQLite_1.0.0       
[10] S4Vectors_0.6.0      BiocGenerics_0.14.0  GenomeInfoDb_1.4.1  
[13] stats4_3.2.1         bitops_1.0-6         XML_3.98-1.2