Where To Find Annotation File For Agilent Microarray?

An easier way that has [probably] only come about since this question was posted is via biomaRt in R.

You can build annotation tables for Agilent 4×44 arrays for mouse and human as follows:

require(biomaRt)

Homo sapiens

# agilent_wholegenome_4x44k_v1
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v1',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))


# agilent_wholegenome_4x44k_v2
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v2',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))

Mus musculus

# agilent_wholegenome_4x44k_v1
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('mmusculus_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v1',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'mgi_symbol'))

# agilent_wholegenome_4x44k_v2
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('mmusculus_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v2',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'mgi_symbol'))

You can view other Agilent tables accessible via biomaRt like this:

listAttributes(mart)[grep('agilent', tolower(listAttributes(mart)[,1])),]
                                name                            description
126                  agilent_cgh_44b                  AGILENT CGH 44b probe
127                 agilent_gpl26966                 AGILENT GPL26966 probe
128                  agilent_gpl6848                  AGILENT GPL6848 probe
129    agilent_sureprint_g3_ge_8x60k    AGILENT SurePrint G3 GE 8x60k probe
130 agilent_sureprint_g3_ge_8x60k_v2 AGILENT SurePrint G3 GE 8x60k v2 probe
131              agilent_wholegenome              AGILENT WholeGenome probe
132     agilent_wholegenome_4x44k_v1     AGILENT WholeGenome 4x44k v1 probe
133     agilent_wholegenome_4x44k_v2     AGILENT WholeGenome 4x44k v2 probe
            page
126 feature_page
127 feature_page
128 feature_page
129 feature_page
130 feature_page
131 feature_page
132 feature_page
133 feature_page

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