I would like to report 2 issues, the first one is a typo, the second one is suggestion to change the default behavior:
1) The _Details_ in the documentation of lmFit()
still says that the default correlation is 0.75, see here: https://code.bioconductor.org/browse/limma/blob/RELEASE_3_21/man/lmFit.Rd#L60
However, that has changed since this commit: https://code.bioconductor.org/browse/limma/commit/f5ccbb95fc8f96ec5ad7f7be9ff582e321f717c1 and it throws an error if correlation
is not specified, see https://code.bioconductor.org/browse/limma/blob/RELEASE_3_21/R/lmfit.R#L72. I believe this should be corrected by removing the 0.75 value and its caveats from the help.
2) Currently in lmFit()
there is no default value for correlation
https://code.bioconductor.org/browse/limma/blob/RELEASE_3_21/R/lmfit.R#L2. However in gls.series()
the default is correlation = NULL
and that causes it to estimate it with duplicateCorrelation()
, see https://code.bioconductor.org/browse/limma/blob/RELEASE_3_21/R/lmfit.R#L240. This is very convenient and my suggestion would be to change to this default behavior in lmFit()
too.
Thank you in advance for your consideration.