broadinstitute/protigy

Proteomics Toolset for Integrative Data Analysis

protigy's Issues

Analysis with only selected columns

Since the recent update, which includes the option to chose Experiment or group column for testing, I can't seem to do statistical tests on only a few selected replicates (to leave out dropouts for example).
If I do not fill in the experiment column in the experimental design file it still includes this sample in the analysis.
Previously leaving the experimental column cell blank for a sample excluded it from analysis.
Is there a new way of doing this?

Example:
When trying to exclude one replicate from one experiment it puts that sample as an unnamed experiment with one sample in (see first attached screenshot).
Then I get this error when I try to run a moderated t test:
Warning: Error in apply: dim(X) must have a positive length

Example 2:
See 2nd attached screenshot of 8 unwanted samples being included together as unnamed experiment.

Excel table creating problem

Deat ProTIGY team,

I have encountered an issue after analyzing the data that the excel table cannot be created and exported.
Do you have any solution/suggestion for this? It suggested that the Perl might be the problem, but I am sure I have Perl installed on the PC and I never had this problem before.
Thanks very much!

Best,
Feng

corrupted file when trying to open app

shiny::runGitHub("protigy", "broadinstitute")
Downloading https://github.com/broadinstitute/protigy/archive/HEAD.tar.gz
Warning in list2(...) : restarting interrupted promise evaluation
Warning in list2(...) : internal error -3 in R_decompress1
Error in list2(...) :
lazy-load database '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cachem/R/cachem.rdb' is corrupt

Error uploading txt file

Hi Karsten,

I was testing protigywith a local installation on my computer but got an error loading the data:

shiny::runApp('~/sandbox/protigy')

Listening on http://127.0.0.1:7377
Warning: Good news!
You don't need to call `useShinyalert()` anymore. Please remove this line from your code.
If you really want to pre-load {shinyalert} to the UI for any reason, use:
        `useShinyalert(force = TRUE)`
---------------------------------
No session id found: 
creating session id...
session: ytiwq635079325 
---------------------------------
Warning in dir.create(global.param$session.dir) :
  cannot create dir '/shiny-data/ytiwq635079325', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/shiny-data/ytiwq635079325/1497_P36-38_all_plexes_bridge_normalized_intensity_sum.tsv', reason 'No such file or directory'
Warning in file(con, "r") :
  cannot open file '/shiny-data/ytiwq635079325/1497_P36-38_all_plexes_bridge_normalized_intensity_sum.tsv': No such file or directory
Warning: Error in h: error in evaluating the argument 'x' in selecting a method for function 'grep': cannot open the connection
  1: shiny::runApp

Any idea on how to solve this? It seems to be a paths issues but I have no idea of what's causing it.

Cheers.

error in downloading protigy through shiny in R

shiny::runGitHub("protigy", "broadinstitute")
Downloading https://github.com/broadinstitute/protigy/archive/master.tar.gz
Error in utils::download.file(url, method = method, ...) :
download from 'https://github.com/broadinstitute/protigy/archive/master.tar.gz' failed
In addition: Warning message:
In utils::download.file(url, method = method, ...) :
URL 'https://codeload.github.com/broadinstitute/protigy/tar.gz/master': Timeout of 60 seconds was reached

Can anyone help me with this, please !