Comments (1)
I was able to reproduce this problem using v1.6.0 of biotmle
from Bioconductor 3.8. Please note that this is happening because of a difference between the development version of biotmle
and the version of the package available from the 3.8 release of Bioconductor. To clarify, this happens because v1.6.0 of biotmle
does not include the accessor function toptable
(here in the development version v1.7.2 of biotmle
on GitHub master
) --- as such, the call to toptable
above is actually calling the wrong function, namely limma::toptable
(and not biotmle::toptable
).
To use the native toptable
accessor function from biotmle
, consider installing v1.7.2 of the packages from GitHub via
remotes::install_github("nhejazi/biotmle@master")
Alternatively, note that the toptable
accessor function is a convenience, and the same output may be extracted by a call that explicitly uses @
to access the appropriate slot. Thus, to extract the same information from your currently installed version of biotmle
, please consider using
head(limmaTMLEout@topTable)
Please feel free to re-open this issue if this does not resolve your current problem. Hope this helps.
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