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ScienceParkStudyGroup / rna-seq-lesson

A Carpentries-style lesson on RNA-Sequencing
https://scienceparkstudygroup.github.io/rna-seq-lesson/
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scripts/mypca.R #13

Closed mocherry closed 3 years ago

mocherry commented 3 years ago

Dear ScienceParkStudyGroup-Team,

I am struggling with your Introduction to RNA-seq lessons. I managed to start a RStudio instance in the browser and now tried to follow Episode 05. However I got stuck at the very beginning when I try to execute: source("scripts/mypca.R") This is followed by an error: Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'scripts/mypca.R': No such file or directory

My this is a trivial problem, but I cannot figure out where it comes from.

Help would be appreciated Thanks and best, Matthias

mgalland commented 3 years ago

Hello @mocherry that's an easy fix for you hopefully.

Normally, the Docker rnaseq-2021 image that is referenced in the Setup section of the lesson should contain the scripts/mypca.R file. I checked and it does not. My bad.

For now, you can either use the Docker rnaseq-latest image with docker pull scienceparkstudygroup/master-gls:rnaseq-latest. I will fix and make a stable image later this month.

In the meantime, if you prefer not to use Docker, here is the link to the mypca.R script. Save it and source it to load the mypca function.

All the best Marc

mgalland commented 3 years ago

The code is now visible and available at https://scienceparkstudygroup.github.io/rna-seq-lesson/extra_functions/index.html#1-custom-pca-function

This will help in case someone wants to follow the lesson locally without the rnaseq Docker image and its embedded mypca.R script.