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DrCytometer / Simplified-flowcytoscript

A simplified, semi-automated high parameter workflow for people who don't know how to code. High dimensional flow cytometry analysis.
GNU General Public License v3.0
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FlowCytoscript Clustering Step Error #1

Open si-purple opened 1 month ago

si-purple commented 1 month ago

Error in FUN(newX[, i], ...) : arguments must have same length 7. stop("arguments must have same length") 6. FUN(newX[, i], ...) 5. apply(dmrd.data, 2, tapply, dmrd.event.cluster, median) at flowcytoscript_clustering.r#271 4. eval(ei, envir) 3. eval(ei, envir) 2. withVisible(eval(ei, envir)) 1. source(file.path(fcs.src.dir, "flowcytoscript_clustering.r"))

The code runs up until it asks for which cell types we have present, then throws an error at this stage!

We know it's running okay until then because it gives us this confirmation of sample sizes:

        **Now we'll match the data files to the group names you entered earlier.
        Files per group:

        flow.sample.condition
        Sample1 Sample2 
            1     1 

        Events per group:

         Sample1  Sample2 
        141311 106418 

        Events per sample:

        Sample1.01 Sample2.01 
          141311   106418 
        Now we'll match the data files to the group names you entered earlier.**
DrCytometer commented 1 month ago

Thanks for this. If you save the markdown file, it produces an html document with all of the stuff you’ve entered. Would you be able to share this html doc with me? This would help me troubleshoot.

DrCytometer commented 2 days ago

si-purple, is it possible you're trying to re-run the analysis in the same folder after it has failed? If so, clear out the cache files (or, better, everything except the flowcytoscript and 00_source_files folder).