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.
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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
... ... ... ... ... ... ... ...