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leekgroup / phenopredict

Use gene expression to predict phenotype sample information
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Vignette example gives different result #4

Closed idontgetoutmuch closed 7 years ago

idontgetoutmuch commented 7 years ago

The vignette has

# number of regions in expression data 
nrow(cm)
## [1] 500
# number of samples included in example
ncol(cm)
## [1] 4769

but I get

> data(sysdata, package='phenopredict')
> nrow(cm)
[1] 100
> ncol(cm)
[1] 100
idontgetoutmuch commented 7 years ago

This confirms what I find

> load("biofinder/phenopredict/data/sysdata.rda", ex <- new.env())
> ls.str(ex)
cm :  num [1:100, 1:100] 19.1 21.7 15.8 15.9 11 ...
cm_new :  num [1:100, 1:100] 12.67 13.18 13.32 7.52 9.4 ...
pheno : 'data.frame':   100 obs. of  109 variables:
ShanEllis commented 7 years ago

Great catch. I never updated pushed the correct one after making the example data smaller/simpler. Doh. Thanks for letting me know! Updated now -- please let me know if you still find discrepancies.

idontgetoutmuch commented 7 years ago

LGTM 👍 thanks :)