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:
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
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).
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'.
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
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).
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'.