problem with preprocess_COSMOS_signaling_to_metabolism

[jytan01]

Hello,

I am trying the tutorial for COSMOS. The forward run completed with no problem using the toy_sif example provided. Now, if I try to replace the toy_sif with meta_sif loaded as meta_sif<-load_meta_pkn(), I get this error when I run preprocess_COSMOS_signaling_to_metabolism():

test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = meta_sif,
                                                      signaling_data = toy_signaling_input_carnival_vec,
                                                      metabolic_data = toy_metab_input_carnival_vec,
                                                      diff_expression_data = toy_RNA,
                                                      maximum_network_depth = 15,
                                                      remove_unexpressed_nodes = T,
                                                      CARNIVAL_options = my_options )

Error:

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
[1] "COSMOS: all 15 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 10 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 259 of the 385 genes in expression data were found as transcription factor target"
[1] "COSMOS: 259 of the 5303 transcription factor targets were found in expression data"
[1] "COSMOS: removing unexpressed nodes from PKN..."
[1] "COSMOS: 74966 interactions removed"
[1] "COSMOS: 4 input/measured nodes are not in PKN any more: XMetab__124886___c____, XMetab__107738___m____, XMetab__190___c____, XMetab__6132___m____ and 0 more."
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 594 from  5650 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 2114 from  5056 interactions are removed from the PKN"
[1] "COSMOS: 5 input/measured nodes are not in PKN any more: X4150, X10379, X9575, X8625, X26298 and 0 more."
[1] "COSMOS:  109 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
Writing constraints...
Error in write_constraints_6(variables = variables, dataMatrix = dataMatrix,  : 
  object 'cc1' not found

The same error is encountered in preprocess_COSMOS_metabolism_to_signaling, this time with toy_sif and meta_sif:

test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_sif,
                                                       signaling_data = toy_signaling_input_carnival_vec,
                                                       metabolic_data = toy_metab_input_carnival_vec,
                                                       diff_expression_data = toy_RNA,
                                                       maximum_network_depth = 15,
                                                       remove_unexpressed_nodes = F,
                                                       CARNIVAL_options = my_options )

Error:

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
[1] "COSMOS: all 15 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 10 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 259 of the 385 genes in expression data were found as transcription factor target"
[1] "COSMOS: 259 of the 5303 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 184 from  720 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 343 from  536 interactions are removed from the PKN"
[1] "COSMOS: 8 input/measured nodes are not in PKN any more: XMetab__6029___l____, XMetab__124886___c____, XMetab__107738___m____, XMetab__6426851___c____, XMetab__700___c____, XMetab__6029___e____ and 2 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
Writing constraints...
Error in write_constraints_6(variables = variables, dataMatrix = dataMatrix,  : 
  object 'cc1' not found

Any help would be much appreciated. Thank you.

[gabora]

Hi @jytan01 ,

this is a known issue in the CARNIVAL dependency and was fixed a few months ago. I am not sure if the Bioconductor version has the fix already, so please install CARNIVAL from our Github repo: https://github.com/saezlab/CARNIVAL thanks Attila

[jytan01]

That worked, thanks!