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DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
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Can singscore handle missing values #30

Open evrama opened 3 years ago

evrama commented 3 years ago

I am exploring your tool to score a bidirectional signature in my proteomics data. Can singscore handle missing values in the expression matrix? I tried and I am getting NAs in the score output

bhuvad commented 3 years ago

Hi @evrama,

Singscore cannot be used with missing values in the matrix as it is as it was primarily designed for use with transcriptomic data. For proteomic data, you could use a workaround whereby you score each sample independently while removing NAs. The method would hold mathematically if you do so. I am keen to integrate this in the future too since proteomics data is becoming more readily available now. I will work on adding this as a feature ASAP (though it may take a few weeks to get it done). I would recommend using the workaround I suggested in the meantime. I will notify on this post once that feature is integrated.

Cheers, Dharmesh.

AJ714 commented 1 year ago

Hi, and thanks for a great tool! I was wondering if there have been any advances with respect to the handling of proteomic data? As by now, I am following the recommended workaround mentioned above, removing NAs for each sample before ranking and scoring. However, having a rather large amount of samples, I would really appreciate to find a more integrated solution in singscore for this kind of data. Cheers,