AnnotationData Packages for Agilent microarrays

https://support.bioconductor.org/p/124640/

I am using Agilent's Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Probe Name Version) (GPL14550), Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) (GPL4133) and Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version) (GPL16699). I cannot find AnnotationData Packages for either of these. Is there any package I could use instead (i.e. HsAgilentDesign026652.db for example?) How could I create a package myself using SQLForge? Is it recommended? Thank you in advance for any help provided.

In my experience, if you use limma to read in the data, you already get the annotation in the 'genes' slot of the EList object, so you usually don't need an annotation package.

Failing that, you can always use GEOquery to get the annotation from the GPL:

z <- getGEO("GPL14550") Table(z)[10000:10005,1:10] ID SPOT_ID CONTROL_TYPE REFSEQ GB_ACC GENE 10000 A_23_P133536 A_23_P133536 FALSE NM_144647 NM_144647 133690 10001 A_23_P133543 A_23_P133543 FALSE NM_017415 NM_017415 26249 10002 A_23_P133582 A_23_P133582 FALSE NM_004730 NM_004730 2107 10003 A_23_P133585 A_23_P133585 FALSE NM_001799 NM_001799 1022 10004 A_23_P13359 A_23_P13359 FALSE NM_006362 NM_006362 10482 10005 A_23_P133596 A_23_P133596 FALSE NM_013235 NM_013235 29102 GENE_SYMBOL GENE_NAME UNIGENE_ID 10000 CAPSL calcyphosine-like Hs.55150 10001 KLHL3 kelch-like 3 (Drosophila) Hs.655084 10002 ETF1 eukaryotic translation termination factor 1 Hs.483494 10003 CDK7 cyclin-dependent kinase 7 Hs.184298 10004 NXF1 nuclear RNA export factor 1 Hs.523739 10005 DROSHA drosha, ribonuclease type III Hs.97997 ENSEMBL_ID 10000 ENST00000513623 10001 ENST00000309755 10002 ENST00000360541 10003 ENST00000256443 10004 ENST00000533048 10005 ENST00000265075

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