Proprecessing expression data into ubiquityScore for mCADRE

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boyu jiang

Mar 12, 2023, 11:50:38 PMMar 12
to COBRA Toolbox

With more exploration of the tutorial of extractionTranscriptomic and testing my own transcriptomic data, I found it a little confusing about how to prepare the input file of UbiquityScore. I have got similar expression data as that of the dataEcoli.mat, but I have no idea how to get the option.ubiquityScore form expression data in dataEcoli.mat. 

I have run "expressionRxn = mapExpressionToReactions(model, expression)", but the output was different from that of the options. ubiquityScore, which contains different values and even negative value(-0.0833). Also, I have tried the procedure on the original paper of mCADRE, but still got a different ubiquityScore.

Could you please give me some clues about this issue? It will be of great help to me, thank you so much!


Ronan M.T. Fleming

Mar 21, 2023, 3:31:58 PMMar 21
Hi Boyu,
why not try something newer:


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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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School of Medicine,
National University of Ireland, Galway.
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Leiden Academic Centre for Drug Research,
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