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I get a mavolcanoplot error and am not sure what it means

Asked by James Quinn on 19 Oct 2018
Latest activity Commented on by James Quinn on 20 Oct 2018
What is meant by holes? Error using message Error filling holes for bioinfo:mavolcanoplot:InvalidPVCutoff. Floating point numbers are not allowed as holes. They should be converted to character vectors.
Error in mavolcanoplot>check_inputdata (line 1466) warning(message('bioinfo:mavolcanoplot:InvalidPVCutoff', paramStruct.pvCutoff));
Error in mavolcanoplot (line 111) [X, Y, PV, paramStruct] = check_inputdata(X, Y, PV, paramStruct);


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1 Answer

Answer by Arthur Goldsipe on 20 Oct 2018
 Accepted Answer

I looked at the code for this function. It looks like you are are getting the wrong error message due to a bug in the Bioinformatics Toolbox. You should have received a warning that the value for the PCutoff option is invalid, and that the default of 0.05 will be used. If you specified the value for PCutoff, make sure that it is between the minimum and maximum values in your dataset.
If you did not specify a value for PCutoff, then perhaps you are encountering another issue. It looks like this warning would be issued if all your PValues are greater than 0.05 or if all your PValues are less than 0.05.

  1 Comment

I think my p values imply insignificance. Thanks.

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