Jing Yu
and 1 contributors

NAME

MultiSkan - The great new MultiSkan!

VERSION

Version 0.02

SYNOPSIS

Used Multiskan Microplate Photometer (Thermo Scientific) for your experiment?

Just got a text file as your output?

Thinking it would be good if it had an app to give you an overview of all wells, and to help to group the data and do some simple stats for you?

GOOD! That means I'm not alone. This module does some simple tasks for you...

    use MultiSkan;
    
    my @groups = (
        'amp', 'A2B2C2',
        'tet', 'A4B4C4',
        'Blank', 'A1B1C1',
 
    );
    my $data_file = 'GrowthCurve.TXT';
    open my $fh, '<', $data_file;
    my $ms = MultiSkan->new(fh => $fh);
    my $A1 = $ms->A1; # quering well A1

You can use

    my %data = $ms->group_stats(@groups); 

to get the averages and standard deviations for each groups. Well, you can use `my @groups = qw/.../`, but then you lose the ability to comment out the groups you don't want for the final report...

If you want to write the data to a file to be processed by other apps (which usually require the data to be arranged in a column-wise fashion, then you can use this snippet:

    my @time = @{$ms->time};
    @time = map {$_/60} @time;
 
    my %data = $ms->group_stats(@groups);
 
    open my $oh, '>', 'report.txt';
 
    print $oh "time";
 
    for (my $i=0;$i<@groups;$i+=2){
        print $oh "\t$groups[$i]\tStdev";
    }
 
    print $oh "\n";
 
 
    for my $i (0..$#time){
        print $oh $time[$i];
        for (my $g=0;$g<@groups;$g+=2){
 
        print $oh "\t".$data{$groups[$g]}->{average}[$i]."\t".$data{$groups[$g]}->{stddev}[$i];
        }
        print $oh "\n";
    }
 

You can use the following function to draw an overview to check out all the 96 wells in a glimpse.

    $ms->draw_all_curves('all_curves.png');

Or you can draw a selected set of data with averages and error bars...

    my %data = $ms->group_stats(@groups);
    $ms->draw_curves(
        'out_img' => 'curves.png',
        'height'  => 768,
        'width'   => 1024,
        'time'    => \@time,
        'data'    => \%data,
        'parameters' => {
            'min_val' => 0,
            'max_val' => 10,
            ...
        },
    );

Since "draw_curves" uses "Chart::ErrorBars" to draw the curves, you can pass all the valid "Chart::ErrorBars" parameters as part of the "parameters" argument.

SUBROUTINES/METHODS

group_stats

This returns the stats (average and stddev) of the groups:

    my %data = $ms->group_stats(@groups);
 

draw_all_curves

Draws a 96-well overview of all the data:

    $ms->draw_all_curves('all_curves.png');
 

draw_curves

Draws curves for the %data returned from group_stats. you can pass any Chart::ErrorBars parameters as a hash ref under `parameters`:

    $ms->draw_curves(
        'out_img' => 'curves.png',
        'height'  => 768,
        'width'   => 1024,
        'time'    => \@time,
        'data'    => \%data,
        'parameters' => {
            'min_val' => 0,
            'max_val' => 10,
            ...
            },
        );
 

AUTHOR

Jing, <logust79 at gmail.com>

BUGS

Please report any bugs or feature requests to bug-multiskan at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=MultiSkan. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc MultiSkan

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2014 Jing.

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.