CRLMM: Which array type work with which annotation package
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4.6 years ago
komal.rathi ★ 3.8k

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 • 1.8k views
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