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Question: CRLMM: Which array type work with which annotation package
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gravatar for komal.rathi
15 months ago by
komal.rathi40
United States
komal.rathi40 wrote:

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!

ADD COMMENTlink modified 15 months ago by Matthew Ritchie690 • written 15 months ago by komal.rathi40
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gravatar for Matthew Ritchie
15 months ago by
Australia
Matthew Ritchie690 wrote:

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 COMMENTlink written 15 months ago by Matthew Ritchie690

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

ADD REPLYlink written 15 months ago by komal.rathi40

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 REPLYlink written 10 months ago by j.holbrook0

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?

ADD REPLYlink written 9 months ago by felix0
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