Question

CRLMM: Which array type work with which annotation package

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komal.rathi ▴ 120

@komalrathi-9163

Last seen 14 months ago

United States

Disclaimer: Crossposted on Biostars.

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 • 2.0k views

ADD COMMENT • link updated 8.2 years ago by Matthew Ritchie ▴ 1000 • written 8.2 years ago by komal.rathi ▴ 120

score 0 · Answer 1 · 2016-10-05

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Matthew Ritchie ▴ 1000

@matthew-ritchie-650

Last seen 7 months ago

Australia

Thanks for your question. For the HumanOmniExpress-24v1-1 and HumanOmniExpress-24v1-0 we don't have a package at this stage unfortunately.

We are putting together a work around for cases like this, where the user specifies the annotation and sets cdfName="nopackage" but I've just identified some bugs in this code, so need to test it out a little more before committing it to Bioconductor.

ADD COMMENT • link 8.2 years ago Matthew Ritchie ▴ 1000

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Thanks for the response. A documentation on the columns required in the custom annotation would be really helpful as well.

ADD REPLY • link 8.2 years ago komal.rathi ▴ 120

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Hi Matthew

I was wondering if you have been able to release the workaround? I have HumanOmniExpress-24v1-2 data I would love to process in crlmm. Thanks!

ADD REPLY • link 7.7 years ago j.holbrook • 0

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Hello,

I would also be interested to know whether I could use the "HumanOmni2-5-8v1-3", as there is as far as I can see no package for that availible yet? How could I import those arrays?