MSstats some R packages failed to download

MSstats some R packages failed to download bandgara22  2024-04-17 00:59

Hello, sir. I am facing to a problem downloading R packages . after multiple trials, some R packages cannot be downloaded in MSstats downloding.

Nick Shulman responded:  2024-04-17 07:29
This seems to work for me.

Can you send me all of the text from the Immediate Window in Skyline? That will probably have a more detailed message about what went wrong.
You can right-click on the Immediate Window and choose "Select All" and then "Copy".
-- Nick
bandgara22 responded:  2024-04-17 09:40
Thank you, sir, for your quick response.
i am mentioning below what was there in the immediate window.

(text moved to attached file "ImmediateWindow1.txt")
Nick Shulman responded:  2024-04-17 10:48
That is strange.
It might be that something was wrong with the internet and if you try this again it will succeed.
Do you have an IT department that might somehow be interfering with files that your computer tries to download?

The R script that Skyline is running to install these packages is here:

If you know how to use R you can run R version 4.2.2 and execute that script. If you are able to successfully run that script yourself then Skyline will notice that all of the necessary packages are installed and Skyline will not need to run that script when installing the MSstats external tool.
It is important that you user R version 4.2.2 to do this (you might have multiple versions of R installed on your computer) because that is the version that MSstats uses and so that's where the packages need to be installed.
-- Nick
bandgara22 responded:  2024-04-18 11:18
sir as per you said i tried it works but as per tutorial said for group comparison i tried but the MSstats group comparison window not seem like as in tutorilas pdf . and i am facing another one problem which is palsted below.

(text moved to attachment "ImmediateWindow2.txt" --Nick)
Nick Shulman responded:  2024-04-18 12:01
It does seem that the MSstats external tool is not working right now. I will try to figure out what is going on with that.

In the meantime, there are many other ways of doing group comparisons in Skyline.
In the Grouped Studies tutorial, starting on page 63 ("Simple group comparisons in Skyline") it talks about how to use Skyline's implementation of group comparisons.
Skyline's implementation is almost as good as MSstats, except that it does not know how to do the statistics for paired controls that are necessary for time series datasets.

Other people use MSstats by exporting a report to a CSV file and then running MSstats in R themselves.
There is also something called MSstatsShiny that some other people use.
-- Nick