Question: AnnotationData Packages for Agilent microarrays
1
gravatar for Alexander Azarian
9 weeks ago by
Armenia
Alexander Azarian20 wrote:

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

ADD COMMENTlink modified 9 weeks ago by James W. MacDonald51k • written 9 weeks ago by Alexander Azarian20
Answer: AnnotationData Packages for Agilent microarrays
2
gravatar for James W. MacDonald
9 weeks ago by
United States
James W. MacDonald51k wrote:

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
ADD COMMENTlink written 9 weeks ago by James W. MacDonald51k
1

James I really need to thank you for your imediate response. You have been really helpfull. I still need to have some genes annotated with ENTREZ Gene ID or Unigene, not just ENSEMBLE IDs. I shall find a way to make this correspondance. Thank you again

ADD REPLYlink written 9 weeks ago by Alexander Azarian20
1

The GENE column in the output is the Entrez Gene ID (which btw is a deprecated term, NCBI dropped the Entrez part several years ago, and just calls it the Gene ID, hence the column name).

ADD REPLYlink written 9 weeks ago by James W. MacDonald51k

Fri, 04 Feb 2011 Entrez Gene is now just plain Gene

You may have noticed that our home page is no longer entitled Entrez Gene. The term Entrez was removed to make the database name be consistent with the URL and other named links within NCBI. We are still in the process of replacing 'Entrez Gene' with 'Gene' in our documents, so the transition is not complete. And of course, we will still respond if called by 'Entrez Gene'.

ADD REPLYlink written 9 weeks ago by James W. MacDonald51k
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