Bioconductor *.db annotation packages
The best place to commence is the listing of Bioconductor annotation packages:
You would then use these .db packages to annotate the probes from each array, for example, hgu133a.db, hgu95av2.db, et cetera*:
library(hgu95av2.db)
mapIds(
hgu95av2.db,
c('991_g_at','976_s_at','954_s_at', 'hhh', '39167_r_at'),
keytype = 'PROBEID',
column = 'SYMBOL')
991_g_at 976_s_at 954_s_at hhh 39167_r_at
"FLT1" "MAPK1" "PPP1CA" NA "SERPINH1"
Both Affymetrix and Illumina annotations are prominent in Bioconductor.
biomaRt
We can also use biomaRt, and I elaborate on an example here:
To retrieve a list of potential annotations in biomaRt, e.g., for Affy, use:
listAttributes(mart)[grep('affy', listAttributes(mart)[,1]),]
name description page
104 affy_hc_g110 AFFY HC G110 probe feature_page
105 affy_hg_focus AFFY HG Focus probe feature_page
106 affy_hg_u133a AFFY HG U133A probe feature_page
107 affy_hg_u133a_2 AFFY HG U133A 2 probe feature_page
108 affy_hg_u133b AFFY HG U133B probe feature_page
109 affy_hg_u133_plus_2 AFFY HG U133 Plus 2 probe feature_page
110 affy_hg_u95a AFFY HG U95A probe feature_page
111 affy_hg_u95av2 AFFY HG U95Av2 probe feature_page
112 affy_hg_u95b AFFY HG U95B probe feature_page
113 affy_hg_u95c AFFY HG U95C probe feature_page
114 affy_hg_u95d AFFY HG U95D probe feature_page
115 affy_hg_u95e AFFY HG U95E probe feature_page
116 affy_hta_2_0 AFFY HTA 2 0 probe feature_page
117 affy_huex_1_0_st_v2 AFFY HuEx 1 0 st v2 probe feature_page
118 affy_hugenefl AFFY HuGeneFL probe feature_page
119 affy_hugene_1_0_st_v1 AFFY HuGene 1 0 st v1 probe feature_page
120 affy_hugene_2_0_st_v1 AFFY HuGene 2 0 st v1 probe feature_page
121 affy_primeview AFFY PrimeView probe feature_page
122 affy_u133_x3p AFFY U133 X3P probe feature_page
Agilent array annotations are also in biomaRt.
Hail Mary / Last resort solution
...as a last resort, you'll often find an annotation CSV or TSV on the array manufacturer's website that you can download, parse, and use.
Kind regards,
Kevin
