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Question: CRLMM: Which array type work with which annotation package
0
2.0 years ago by
komal.rathi50
United States
komal.rathi50 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
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"
[9] "human550v3b"             "human1mduov3b"
[13] "humanomni258v1a"         "humanomni258v1p1b"
[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!

modified 2.0 years ago by Matthew Ritchie730 • written 2.0 years ago by komal.rathi50
0
2.0 years ago by
Australia
Matthew Ritchie730 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.

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

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!

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?