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nolanlab / citrus

Citrus Development Code
GNU General Public License v3.0
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Running citrus on groups with only one fcs. file #37

Open cjla87 opened 10 years ago

cjla87 commented 10 years ago

It would be useful to detect batch effects by comparing the same sample run in different batches but currently citrus doesn't run if there is only one file in a group.

rbruggner commented 10 years ago

If you have a bunch of samples measured on different days and want to see batch effects, you can use the day of measurement as the sample group and check for differences. However, Citrus is not really able to detect unspecified trends between samples (i.e. unspecified batch effects). Also, it is not currently able to detect differences between single (or very small numbers) samples - I'm not quite sure what the appropriate statistical measure of "differences" would be without replicates.

Frequency difference gating, flow fingerprinting, and some other methods have attempted to systematically look at questions of QC or differences between pairs of samples.