Here is the details regarding to the bug fix related to the sorting behavior of 'read.flowSet':
I think it had been sorting samples in the older version which you were probably not aware of. The latest version just makes sure the sampleNames of flowSet and the actual sample data (flowFrames) are in sync .
If the default alphabetic order is not what you want, you can always reorder it by 'fs[ind]', where 'ind' is the numeric index that you should be able easily derive from your original file input list.
From: David Knapp [email@example.com]
Sent: Thursday, July 30, 2015 10:51 AM
To: Jiang, Mike
I've been using flowCore for some time for my analyses. I've recently noticed (presumably with the last update) that the read.flowSet function no longer maintains the order of the file vector given to it but instead automatically sorts on file name. This behaviour is increadibly annoying and makes the function completely unusable to me as I need my flowSets to be in the specified order.
Please at least put an option to not sort back in. Thanks.