Error in creating a volcano plot in MATLAB

I am a complete newbie to MATLAB and the first task I have is to create a volcano plot. I have been using the documentation to understand about it and get started.

I tried to run it on dummy values -

a=[1 2 3]
b=[4.6 2.7 4.5]
c=[0.05 0.33 0.45]

And then I ran -

SigStructure = mavolcanoplot(a, b, c)

My understanding is that a represents the gene expression values for condition 1, b for condition 2, and c is the list of p-values for the 3 data points in a and b.

However running this code gives me the error -

Index exceeds matrix dimensions.

Error in mavolcanoplot (line 127)
appdata.effect = X(paramStruct.goodVals) - Y(paramStruct.goodVals);

Error in volc (line 4)
SigStructure = mavolcanoplot(a, b, c)

Can anyone explain where I am going wrong?

Solution

You're encountering an issue because you are using row vectors.

Inside the mavolcanoplot function (you can see the file by typing edit mavolcanoplot in the command window) there is a local function for checking the inputs, called check_inputdata.

Your data passes all of the validation checks, and then encounters this section:

% Here, 'X' and 'Y' are the local names for your inputs 'a' and 'b'
% Below code is directly from mavolcanoplot.m:

% Handle the matrix input. Use its mean values per row
if size(X, 2) > 1
    X = mean(X,2);
end    
if size(Y, 2) > 1
    Y = mean(Y,2);
end

This reduces your inputs to their mean. Later in the main function (line 127) you encounter the error as described, where paramStruct.goodVals is a 3 element array, which is now trying to index a 1 element array and fails!

This is basically a lesson in debugging and reading the documentation, which states

DataX, DataY: If a [...] matrix, each row is a gene, each column is a sample and an average expression value is calculated for each gene.

You should use one of these equivalent methods to create column vector inputs

a=[1 2 3].';       % Using transpose (.') to create a column vector from a row vector
b=[4.6; 2.7; 4.5]; % Creating a column vector using the semi-colon operator to end each row
c=[0.05
   0.33
   0.45];          % Using actual code layout to create a column vector