Hello Shimin,
Thank you for bringing this to our attention. You are not missing any steps, this was a bug inside Skyline Batch. It has since been fixed in Skyline Batch-daily, which you can download by uninstalling your current version of Skyline Batch and reinstalling from https://skyline.gs.washington.edu/software/SkylineBatch-daily/index.html. The main release of Skyline Batch will be updated with the bug fix soon, so
keep an eye out for updates if you decide not to switch to Skyline Batch-daily.
Please let us know if the problem persists after installing Skyline Batch-daily or updating the program (when the new update becomes available).
Thanks,
Ali

Hi Ali,

Thank you very much for your help!

Best,
Shimin

Hello Skyline team,

I decided to add to this existing thread, since I also seem to have an R-related problem within Skyline Batch (SB), albeit a different one. I am trying to implement the whole Skyline Batch process for MRM data analysis, from importing raw data to exporting a report called 'MRMNormalizeR.csv' and running an R script with it. Everything seems fine until R starts, but then I am getting an error message:

ERROR: Error in file(file, "rt") : cannot open the connection
[19/12/2022 13:05:59] Calls: read.csv -> read.table -> file
[19/12/2022 13:05:59] In addition: Warning message:
[19/12/2022 13:05:59] In file(file, "rt") :
[19/12/2022 13:05:59] cannot open file 'MRMNormalizeR.csv': No such file or directory

It seems that R cannot find the exported report, however, SB is definitely creating it in the Analysis folder, where also the R script is located. The exported report is totally fine by itself and I can run the R script without problems using R Studio. However, it does not run within SB. I tried it with SB 21.2.0.389 and with 21.2.1.389. Is this issue known? I am attaching a log file and I am happy to provide more data but would rather upload it via a private link, if possible.

Thanking you in advance,
Roman

Hi Roman,
I guess I would alter the R script to output the full path to the CSV file just before your call to read.csv. It seems strange to me that the error message is only mentioning the file name, and not its full path.

I think you need a bit more debug output to be completely sure that the expected values are making it to the right place, or if not, why not.

This line in your log file:

[19/12/2022 12:17:54] "C:\Users\Roman Sakson\Documents\Roman\PhD\PhD\Paper\Analytical_Chemistry\Manuscript\Data\Skyline_Batch\Analysis_Folder\22.11.12_MRM_GroupComp_Plotting_RS_Batch_FINAL.R" "C:\Users\Roman Sakson\Documents\Roman\PhD\PhD\Paper\Analytical_Chemistry\Manuscript\Data\Skyline_Batch\Analysis_Folder\MRMNormalizeR.csv"

Seems to indicate the Skyline Batch is calling the right R file with the full path. Though, I could imagine it would be helpful to have the entire command line including the path the R.exe used and exactly the parameters on the command line.

Hope this helps. Let us know what you learn. Definitely this pipeline has worked with several different R scripts and reports in our own testing.

--Brendan

Hi Brendan,

yes, you are right, if I explicitly set the working directory then the error seems gone (I added the line 44 in the minimal example that I am attaching

"setwd("C:/Users/Roman Sakson/Desktop/Analysis_Support")"

and it worked, but it does not work without it, even though the csv and the R script are both in the analysis folder.

I need to do some more testing with a second computer to learn in which way file paths are being preserved within a bcfg. I would like to offer a bcfg file to people who know enough Skyline to run it in Skyline Batch but who know virtually no R, ideally enabling them to get R script outputs without having to interact with the code itself (a little bit like the MSstats plugin within Skyline). Let's see, whether this is feasible at the moment.

I might bother you again soon. Thanks for your help!
Roman

Hi Roman,

I had a similar question before and actually found the solution in one of the demo scripts provided by the Skyline team when Skyline Batch/Skyline Command Line was initially introduced. It has been a while and I couldn't find the original code now. Here is what I used in my script:

This R script uses the file path of the Skyline report as the working directory:

script_args <- commandArgs(trailingOnly = TRUE)

isCommand = length(script_args) > 0
if (isCommand) {
  reportPath <- script_args[1]
} else {
  errorCondition("Did not receive a report path argument")
}
reportPath = gsub("\\\\", "/", reportPath)
rootPath = dirname(reportPath) 
setwd(rootPath)

This may be helpful if someone wants to remove the step of manually specifying the working directory. Again, all credits to the Skyline team.

Shimin

Hi Shimin,

thank you, this is very good to know!

Best regards,
Roman

Hi Nick,

well, I am not sure that I would be able to guess what an invariant CSV is (but I am also not really a command line person, as you can easily tell from my struggles here). Not sure what a better wording could be. The normal csv seems to contain the same area numbers that are being displayed in my Skyline document grid, so I hope simply using those for calculations should not introduce too much bias. Are calculations in the background of Skyline being performed on more precise numbers?

I am happy with what Skyline can do and would like to leave MSstats out of it for now. However, the Result File Rules seem to be exactly what I am looking for: to define the condition based on a regular expression within the filename! Thanks a ton, I am getting close but it works for me only within the Skyline GUI but not via SB. Here is what I observe:

1. I am saving my results rule and the custom report within the empty template document.

2. I start my SB configuration, the template document gets copied to the analysis folder and the raw file import occurs.

3. The exported report still contains an empty condition column, so it does not work and R reports an error. When I then open the copied template file from the analysis folder with Skyline 22.2, the condition column from my report is indeed empty, even though the results rule is checked and the Preview shows exactly what I want.

4. I then go to Document Settings... -> Annotations, uncheck Condition and save. Skyline warns me that there is then a problem with the results rule, which I ignore. Then, I again go to Document Settings... -> Annotations, check Condition back on and save again. Now, the results rule kicks in and my custom report gets all the correct Conditions assigned according to the filename. If I would start SB now from the report export step, my R script would work.

There seems to be some kind of a "refresh" command missing for an existing results rule when using SB instead of the GUI. Or, maybe, I am missing a step?

Thank you for your help,
Roman