AnnotationDbi packages missing in current release
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Isaac Neuhaus ▴ 360
@isaac-neuhaus-22
Last seen 7.5 years ago
United States

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

 

htmg430b.db primeview.db htrat230pm.db hthgu133pluspm.db htmg430a.db • 1.8k views
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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>

 

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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/

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Isaac Neuhaus ▴ 360
@isaac-neuhaus-22
Last seen 7.5 years ago
United States

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")
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So does that mean you got it to work or not?

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Yes. Thank you.

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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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