Question: AnnotationDbi packages missing in current release
0
gravatar for Isaac Neuhaus
4.4 years ago by
Isaac Neuhaus360
United States
Isaac Neuhaus360 wrote:

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

 

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Isaac Neuhaus360
1

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>

 

ADD REPLYlink written 4.4 years ago by James W. MacDonald51k

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/

ADD REPLYlink written 4.4 years ago by Marc Carlson7.2k
Answer: AnnotationDbi packages missing in current release
2
gravatar for Isaac Neuhaus
4.4 years ago by
Isaac Neuhaus360
United States
Isaac Neuhaus360 wrote:

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")
ADD COMMENTlink modified 4.4 years ago by James W. MacDonald51k • written 4.4 years ago by Isaac Neuhaus360

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

ADD REPLYlink written 4.4 years ago by James W. MacDonald51k
1

Yes. Thank you.

ADD REPLYlink written 4.4 years ago by Isaac Neuhaus360

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")

 

ADD REPLYlink written 3.9 years ago by thrabe0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 193 users visited in the last hour