Assuming that channelData is a 2-element cell array, that channelData{1} and channelData{2} are both column vectors, and you want to combine them into a matrix with two columns, then you can use trimdata to do so like this:
% n: length of shorter vector
% idx: index (1 or 2) of shorter vector in channelData
[n,idx] = min([numel(channelData{1}) numel(channelData{2})]);
% trim the longer vector (3-idx makes 1 become 2 and vice versa) to length n
channelData{3-idx} = trimdata(channelData{3-idx},n);
% combine the vectors into an n-by-2 matrix
combinedData = [channelData{:}];
If you don't want to overwrite channelData, then use a temporary variable instead:
tmp = channelData;
tmp{3-idx} = trimdata(tmp{3-idx},n);
combinedData = [tmp{:}];
Your mistake was using trimdata to trim the cell array channelData itself rather than the contents of one of its cells (i.e., channelData{1} or channelData{2}, whichever is longer). That and not using the assigned output mycell, so that you were not actually modifying channelData at all before attempting to concatenate its contents.
