The following packages are missing in the current version of Bioiconductor (R): htmg430b.db, primeview.db, htrat230pm.db, hthgu133pluspm.db, htmg430a.db, htmg430pm.db. Is there any way I can create them. I tried using the AnnotationForge package but I was not able to build them with the Affymetrix annotation files.
Thank you.
Isaac
My bad. I figure that I needed to load a couple of libraries before I run makeDBPackage. Here is the procedure:
library(AnnotationForge)
library(org.Rn.eg.db)
library(rat.db0)
makeDBPackage("RATCHIP_DB", affy = TRUE, prefix="htrat230pm",
fileName="HT_Rat230_PM.na35.annot.1.csv", baseMapType="gbNRef",outputDir=".",
version = "12.1.0", manufacturer="Affymetrix",
manufacturerUrl="http://www.affymetrix.com")
Hi Isaac,
I tried your code, but it fails for me. Sorry to bug you, but I am new to all this. I downloaded the CVS of hthgu133, but am getting nowhere with my commands. Can you please help?
library(AnnotationForge)
#library(org.Rn.eg.db)
#library(rat.db0)
makeDBPackage("HT_HG_U133_Plus_PM", affy = TRUE, prefix="hthgu133pluspm.db",fileName="./affymatrix/HT_HG-U133_Plus_PM.na35.annot.csv/HT_HG-U133_Plus_PM.na35.annot.csv", baseMapType="gbNRef",outputDir=".",version = "12.1.0", manufacturer="Affymetrix",manufacturerUrl="http://www.affymetrix.com")
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version 2.3.6
The short answer is 'Use AnnotationForge'. But that is the answer to the (wrong) question. Really you should be asking something like:
I tried to make an annotation package using AnnotationForge, using the following code, but it failed. Can anybody give me some pointers, or explain where I made a mistake?
<code goes here>
<output from sessionInfo() goes here>
And another good tip that might help is to look at the posting guide. Which you can see here:
http://bioconductor.org/help/support/posting-guide/