Missing input file for part 6

[szsctt]

I'm going through the tutorial, and am up to part 6 - analysis of CARNIVAL results. In the first chunk of this part, the results from the previous part are loaded, including a file ../results/carnival_sample_resolution.rds. This file is present in this repository, but isn't saved in any of the previous parts of the tutorial. I'm unsure what this file contains - is it results that are specific to the dataset being analysed? I'm tryinig to use my own data, but I'm not sure if I should use the version of this file that is in this repository, or if I should generate it for my own data. Could you please advise if the file in this repository is general (can be used for any dataset), or if not, how to generate this file for my data?

[ulrmu]

I'd also like to know this! Especially how to create the file using my own data. Can anyone comment?

[rosherbal]

Hi all, Thanks for your comment and sorry for the delay on the response. The file carnival_sample_resolution.rds is the result of running the series of scripts sample_resolution_X.R. It is basically the same, but in this case we run the transcriptutorial for several samples. That is, we get PROGENy, DOROTHEA and CARNIVAL using directly the expression instead of the contrasts. It is done this way to get more than one network, so we can do some network comparisons.

[ulrmu]

@rosherbal Thank you! When I run the sample_resolution_carnival.R script, the following error is raised when trying to execute runCARNIVAL:

Error in checkWeights(weights, nodesPriorKnowledgeNetwork) : 
  Please provide a valid weights object: a vector with identifiers and their values. Or did you use carnivalOptions in place of weights object?

When I comment out weightObj as an input, the runCARNIVAL command executes. Is there any explanation why that happens or how it can be solved?

[ziweihf]

@rosherbal Thank you! When I run the sample_resolution_carnival.R script, the following error is raised when trying to execute runCARNIVAL:

Error in checkWeights(weights, nodesPriorKnowledgeNetwork) : 
  Please provide a valid weights object: a vector with identifiers and their values. Or did you use carnivalOptions in place of weights object?

When I comment out weightObj as an input, the runCARNIVAL command executes. Is there any explanation why that happens or how it can be solved?

Did you follow by this tutorial ？https://github.com/saezlab/transcriptutorial/blob/master/scripts/05_network_reconstruction_with_CARNIVAL.md

carnival_result = runCARNIVAL( inputObj= iniciators, measObj = tfList$t, netObj = sif, weightObj = progenylist$score, solverPath = "/Applications/CPLEX_Studio128/cplex/bin/x86-64_osx/cplex",

solverPath = "/Applications/CPLEX_Studio129/cplex/bin/x86-64_osx/cplex",

                           solver = "cplex",
                           timelimit=60,
                           mipGAP=0,
                           poolrelGAP=0 )

if so, you can try to check the type of progenylist$score (it's a data.frame ). I got the same error. It worked after I changed it into vector