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bschiffthaler / seidr

Toolkit to create crowd networks
GNU General Public License v3.0
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--no-scale possibly not working for correlation and pcor #44

Closed gianfilippo closed 2 years ago

gianfilippo commented 2 years ago

Hi,

very nice package!

I am running a script like in your tutorial. My data are batch corrected and have negative values. Scales are very similar so I am running with the --no-scale flag.

correlation -t $dataDIR/$targetFILE -m pearson -i $dataDIR/$exprFILE -g $dataDIR/$geneFILE -o $outDIR/pearson_scores.tsv --no-scale

pcor -t $dataDIR/$targetFILE -i $dataDIR/$exprFILE -g $dataDIR/$geneFILE -o $outDIR/pcor_scores.tsv --no-scale

The output for both "correlation" and "pcor" still state "Transforming matrix to z-score", though, although it does not throw any error for the --no-scale flag.

Thanks

bschiffthaler commented 2 years ago

You're right, the flag that triggers scaling was invariably true (for all algorithms, including those that do not necessarily output a message - like el-ensemble, genie3 etc.). I'm pushing a fix to the devel branch. If you build from source you can do that asap, otherwise I'm planning a version release via bioconda in January.

Thanks for noticing the issue!

gianfilippo commented 2 years ago

Thanks!