Issue with DGE analysis using ds.limma

Support Developer support
1

Hi, I’m having some issues using the ds.limma function. Specifically, when following :

my output is :

"Command 'limmaDS2(rse, res, 2L, NULL, 2, NULL, FALSE, \"none\")' failed on 'study1': 
Error while evaluating 'dsOmics::limmaDS2(rse, res, 2L, NULL, 2, NULL, FALSE, \"none\")' -> 
Error in dsOmics::limmaDS2(rse, res, 2L, NULL, 2, NULL, FALSE, \"none\") : \n  object 'Set.counts' not found\n"

Troubleshooting:

  • I locally downloaded the dataset used in the guide above
  • I downloaded the code of the ds.limma function (client side) and limmaDS function (server side) available on dsOmics/R at master · isglobal-brge/dsOmics · GitHub and combined them together to run locally on the downloaded dataset.

Running locally produces the expected output (the analysis is correctly executed).
What seems to be the problem is the connection between the two functions when operating in client-server mode, specifically this piece of code when calling limmaDS

Set <- eval(parse(text=Set), envir = parent.frame())
2

Dear Francesco,

Thank you for raising this issue. I have taken a look at the code and traced back the error.

Please note it has been fixed, see commit fix: type not used here · isglobal-brge/dsOmics@9f5fe8c · GitHub.

I have just tested to install this latest version on the “omics” profile of opal-demo.obiba.org and sucessfully run.

Also, seems the document you link should be updated so the builder looks like this

builder$append(server = "study1", url = "https://opal-demo.obiba.org", 
               user = "dsuser", password = "P@ssw0rd", profile = "omics",
               resource = "RSRC.tcga_liver", driver = "OpalDriver")

Anyway, let me know if it is also solved on your end. On the meantime I will get in contact with the maintainer of opal-demo so the latest version of dsOmics is there permanently.

Have a great day,

Xavier.