I am trying to run the DEP analysis of TMTx10 data in shiny app

"run_app("TMT")"

and get the

"Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase' "

I saw in another post on "run_app("LFQ")" this may be due to eror in the original code in the DEP package. It seems it is not fixed yet.

Is there a quick fix for this?

Thanks Shaj

This is a bug that was reported on the issues page for DEP way back in 2021, and is apparently yet to be fixed. I would normally suggest providing a patch to the maintainer, but if the issues page on their GitHub is being ignored, a patch is likely to be ignored as well.

If you just want to get it to work, you can either clone the repo or just download the tar.gz file (see the Package Archives part of the landing page). If you download the tarball, you have to decompress it. If you then navigate to DEP/inst/shiny_apps/TMT/ and open app.R in your favorite text editor (or R IDE), you can look for this code block, and change MSnbase to MsCoreUtils.

menuItem("Imputation options",
                 radioButtons("imputation",
                              "Imputation type",
                              choices = c("man", MSnbase::imputeMethods())[1:9],  <---------------this part right here
                              selected = "MinProb"),
                 p(a("Detailed information link",

You can then install the package by starting R and using install.packages

install.packages(<path to DEP>, repos = NULL)

If you are on Windows, add source = TRUE to that call.