Table 6 |.
Troubleshooting table
Step | Problem | Probable reason | Solution |
---|---|---|---|
2 | Package installation failed | R version is old or dependent package cannot be installed | Update R to 3.5.0 or newer. Try to start the R session from the root folder. The PATH variable can be set by typing into a terminal: For Linux $export PATH="/usr/bin:$PATH" For MacOS $export PATH="/usr/local/bin:$PATH" |
7Avii | MAGeCK crashed with an error related to the design matrix. Such as: “Error parsing the design matrix: 0 row sums for some samples.” |
Design matrix was not in a correct format | Follow the tutorial to generate a correct design matrix. https://bitbucket.org/liulab/mageck-vispr |
7Bv | MAGeCK-VISPR crashed with an error due to cannot find input files: “Error in configuration file (key=library, entry=xxx): File does not exist.” |
File names or paths of the input files is incorrect. | Double check the names and paths of the input files and make sure these files can be accessed. |
11B | FluteMLE crashed with an error due to cannot find samples: “Error in FluteMLE(gene_summary = ‘mle.gene_summary.txt’, treatname = ‘treatment.beta’, : No sample found!” |
The index specified with the parameters “treatname” or “ctrlname” does not fit the column names of “gene_summary.txt” file. | Ignore the suffix “.beta” when specifying the control names and treatment name with the parameter “treatname” and “ctrlname” |