Question: ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, whereas probe.features.epic does not exist
gravatar for line.heylen
3.2 years ago by
line.heylen10 wrote:


I updated R and Bioconductor to use the new ChAMP package for EPIC arrays. In contrast to what is written in the manual, it seems that probe.features.epic does not exist, and that probe.features entails now the EPIC data and not the 450K data. How is this possible? 

> dim(probe.features)

[1] 867531      2

> dim(probe.features.epic)
Error: object 'probe.features.epic' not found

In addition, the probe.features data entails only the columns CHR and MAPINFO and not all the other columns (gene, feature,..) it should have. 

> head(probe.features)
           CHR   MAPINFO
cg07881041  19   5236016
cg18478105  20  61847650
cg23229610   1   6841125
cg03513874   2 198303466
cg09835024   X  24072640
cg05451842  14  93581139

Does anyone know how to solve this? 

Thank you!



champ • 429 views
ADD COMMENTlink written 3.2 years ago by line.heylen10

It seems that if I start R again, and load data(probe.features); it successfully loads the 450K annotation.

If I load the epic annotation by data(probe.features.epic) probe.features refers then to the epic array and not the 450K array, and includes only the first 2 columns. 

ADD REPLYlink written 3.2 years ago by line.heylen10
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