Vince Carey

pp 3-10 of vignette are equal signs showing a download pp 11 doesn't seem to be evaluated it is preferable to use R markdown for vignette although sweave is allowed...

should the data be in a summarized experiment so that the phenotype data are tightly bound to the assay data?

let us know if you plan to revise this submission and if so on what time scale. thank you

there are no commits to the BIoconductor git repo since august 4. push to the remote upstream

While building vignette by hand I hit ``` /home/stvjc/.cache/R/rpx does not exist, create directory? (yes/no): yes ``` I wonder if the vignette should fail at this point, directing the user...

``` > R_user_dir("cache") [1] "/home/stvjc/.local/share/R/cache" ``` seems more standard to me. Also ``` label: unnamed-chunk-23 Quitting from lines 316-319 (MsExperiment.Rmd) Error in .local(object, ...) : Parameter 'files' is mandatory for...

it didn't fail, it just paused during my manual compilation of vignette. as programmed. it just doesn't happen very often. As for cache location, ignore my comment but I expected...

It did fail however at unnamed chunk 23.

Sorry for so many bumps. I thought ``` Quitting from lines 158-160 (MsExperiment.Rmd) Error: processing vignette 'MsExperiment.Rmd' failed with diagnostics: error in evaluating the argument 'object' in selecting a method...

Hi -- this very comprehensively documented package will have to change in certain respects to be part of Bioconductor. I find that the built package is 13MB in size. I'll...