function cellAbs = PlateAbsSubtraction(orderedAbs)

%To use this code, just enter your input file prefix here - 
filename = 'Full Plate Same Media Blank Test';
%and the path to where your data should be saved.  If you don't specify an
%output location, it will  use the current directory.
% outputpath = '~/Desktop/Chassis-System/Data/PlateReader/DedicatedTranslation/';


[TimeDataalpha, LabelDataalpha] = platereaderread2MG(filename);

%%
%============
%set smoothing parameters
%============
method = 'fb';
if method == 'fb' | method == 'ff'
    cutofffreq = 0.15;
    neighbors = [];
elseif method == 'co'
    cutofffreq = 0.15;
    neighbors = 9;
elseif method == 'ma'
    cutofffreq = [];
    neighbors = 9;
end
plotunsmoothalpha = 0;
plotsmoothalpha = 1; 

Absbackgroundsamplesalpha = [];

experimentsamplesalpha = [1,2,3,4];
namesalpha = [];


replicatesalpha = 3;
samplesalpha = [experimentsamplesalpha,Absbackgroundsamplesalpha];
% Extract the data that we are interested in into three new variables.  By
% default, consider all timepoints and wells
% timepoints = [1:size(LabelData,1)-1];
wellsalpha = [1:size(LabelDataalpha,2)];

timepointsalpha = [1:10];

timepointsbeta = [1:99];

% wells = [1:6];


rawAbsalpha = LabelDataalpha(timepointsalpha,wellsalpha,1);
Timealpha = TimeDataalpha(timepointsalpha);

%If your data has a fixed number of replicates for each sample and control,
%and the replicates are in adjacent wells, use this code to reshape both 
%matrices so that the third dimension represents the different replicates
orderedAbsalpha = reshape(rawAbsalpha,[size(rawAbsalpha,1),replicatesalpha,size(rawAbsalpha,2)/replicatesalpha]);
%reorder the dimensions of the array so that the third dimension is the
%number of replicates.
orderedAbsalpha = permute(orderedAbsalpha,[1,3,2]);

orderedAbsalpha = orderedAbsalpha(:,samplesalpha,:);

orderedAbsalpha = mean(orderedAbsalpha(end-3:end,:,:),1)
orderedAbsalpha = repmat(orderedAbsalpha,[max(timepointsbeta),1,1])
 
cellAbs = orderedAbs - orderedAbsalpha;