Error: "supply both 'x' and 'y' or a matrix-like 'x'"

[tsveth]

Hi, first off, thanks for the great developed pipeline!

Currently I am trying to analyze some files. After running the QC functions successfully I start with the quantification using:

artmsQuantification(
  yaml_config_file = "my_config_subset.yaml")

Afterwards I run the following command directing to the output of previous function:

artmsAnalysisQuantifications(log2fc_file = "outputfolder/results.txt",
                             modelqc_file = "outputfolder/results_ModelQC.txt",
                             species = "human",
                             output_dir = "AnalysisQuantifications")

Unfortunately I get the following error:

---------------------------------------------
artMS: ANALYSIS OF QUANTIFICATIONS
---------------------------------------------
--- No Pathogen extra in these samples
>> LOADING QUANTIFICATIONS (-results.txt from MSstats) 
>> LOADING modelqc FILE (ABUNDANCE) 
--- Outliers kept (user selection)
--- Total number of genes/proteins: 5663 
--- Removing log2fc outliers (-15 < log2fc < +15) 
>> IMPUTING MISSING VALUES 
--- Number of +/- INF values: 1167 
--- Plotting distributions of log2fc and pvalues 
>> PLOT: CORRELATION BETWEEN QUANTIFICATIONS (based on log2fc values)
---Total unique identifiers before: 5669
---Total unique identifiers (only complete cases): 3819
  |=================================================================================                                                                                 | 
 50%Error in cor(datadc[[br1]], datadc[[br2]]) : 
  supply both 'x' and 'y' or a matrix-like 'x'

Any ideas what I can do?

Thank you!

[David JM]

Thanks @tsveth

The most frequent cause is the labels used in the keys. Could I take a look at the keys? You could either share the file here (ideal, so other users could benefit) or send it to [e-mail] (if you have any concerns about sharing it publicly)

[tsveth]

David helped me via the mail and solved the problem.

Problem: R does not like it when names start with a digit. One of the names in the keys.txt file was "4378..."

Sollution: "I adjust the digit starting name in the keys.txt file to "S4378..."

Thank you David!

[David JM]

Glad that it got solved! Thanks for sharing!