This tool runs CrossSample using the MFI from FLOCK and text-converted FCS files.

The option chosen for the centroids (mean, median or geometric mean) should be the same as used to run FLOCK. Output Each event within each file of a dataset collection is attributed to a population depending on its intensity profile. A table of the population composition of each file is generated as well as MFI and population descriptive statistics. .. class:: infomark Tip: If headers in each text-converted FCS file do not match those in the centroid file, the program will not run. Edit the input file using the Remove, rearrange and/or rename columns tool in the Flow Text File Tools section prior to Cross Sample analysis. ----- Example Input - fluorescence intensities per marker per event:

Marker1 Marker2 Marker3 ...
33      47      11      ...
31      64      11      ...
21      62      99      ...
14      34      60      ...
...     ...     ...     ...

Centroid file - mean, geometric mean or median fluorescence intensity per marker per population::

Population Marker1 Marker2 Marker3 ... 1 38 49 10 ... 2 21 63 100 ... 3 31 52 45 ... 4 11 78 25 ... ... ... ... ... ...

Output for each text file - fluorescence intensities per marker and population ID per event::

Marker1 Marker2 Marker3 ... Population 33 47 11 ... 1 31 64 11 ... 6 21 62 99 ... 2 14 34 60 ... 7 ... ... ... ... ...

Summary table - distribution of events in each population in each file::

Filename SampleName Pop1 Pop2 Pop3 ... File1 Biosample1 0.1 0.25 0.14 ... File2 Biosample2 0.02 0.1 0.17 ... File3 Biosample3 0.4 0.05 0.21 ... File4 Biosample4 0.05 0.3 0.08 ...

Centroid MFI Summary table - for each file, mean, median or geometric mean fluorescence intensities per marker per population::

Marker1 Marker2 Marker3 ... Population Percentage SampleName 154 885 24 ... 1 0.2 Biosample1 458 74 574 ... 2 0.3 Biosample1 3 210 86 ... 3 0.05 Biosample1 ... ... ... ... ... ... ... 140 921 19 ... 1 0.1 Biosample2 428 79 508 ... 2 0.25 Biosample2 9 225 90 ... 3 0.3 Biosample2 ... ... ... ... ... ... ...

MFI Descriptive Statistics table - for the set of files, mean, median and standard deviation of each centroid per marker per population, as well as mean, median and standard deviation of the population's proportion::

Population Marker1_mean Marker1_median Marker1_stdev ... Percentage_mean Percentage_median Percentage_stdev 1 94.65 90.86 25.8 ... 1.84 0.55 2.48 2 132.18 131.58 5.02 ... 9.89 9.76 0.33 3 71.8 69.68 10.53 ... 3.02 1.49 3.45 4 84.85 84.85 nan ... 8.52 8.52 nan 5 161.82 132.77 61.29 ... 0.95 0.37 1.06 ... ... ... ... ... ... ... ...