CRLMM: Which array type work with which annotation package
0
0
Entering edit mode
7.6 years ago
komal.rathi ★ 4.1k

Disclaimer: Crossposted on Bioconductor.

I am using the CRLMM package. We have about 21000 IDATs that belong to the following array types:

Array                    Annotation Package (Guess)
HumanHap550              human550v3b
Human610-Quad            human610quadv1b
HumanOmniExpress-24v1-1  Not sure
HumanOmniExpress-24v1-0  Not sure
HumanOmniExpress-12v1-1  humanomniexpress12v1b
HumanOmniExpress-12v1-0  humanomniexpress12v1b

These are the annotation packages supported by CRLMM:

> validCdfNames()
 [1] "genomewidesnp6"          "genomewidesnp5"         
 [3] "human1mv1c"              "human370v1c"            
 [5] "human650v3a"             "human610quadv1b"        
 [7] "human660quadv1a"         "human370quadv3c"        
 [9] "human550v3b"             "human1mduov3b"          
[11] "humanomni1quadv1b"       "humanomni25quadv1b"     
[13] "humanomni258v1a"         "humanomni258v1p1b"      
[15] "humanomni5quadv1b"       "humanomniexpress12v1b"  
[17] "humanimmuno12v1b"        "humancytosnp12v2p1h"    
[19] "humanexome12v1p2a"       "humanomniexpexome8v1p1b"

I am not certain which annotation packages (validCdfNames) will go with the human omni express arrays mentioned above. Any help would be much appreciated.

Thanks!

crlmm • 2.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 2976 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6