[BioC] flowClean

[Pratip K. Chattopadhyay]

There are probably a couple of factors at work here...

The HTS is more likely to exhibit anomalies early in collection for 
various reasons... The pressure in the system may still be building up, 
the cells are settled in the bottom of the well and so more events go 
through at once, clogs/debris from previous wells/runs may dislodge.  In 
principle, the system is engineered to avoid these issues, but in 
practice, I often (but not always) see anomalies at the beginning of the 
collection.  Interestingly, on days/runs where there aren't many bad 
regions flagged, the early regions also look good.  This inspires 
confidence that the algorithm is detecting true problems and doesn't 
have some systematic problem.

The second factor - relevant to the case where you felt the first events 
weren't too bad - is guilt by association.  Kipper has built in a little 
buffer to take out some bins that neighbor trouble spots, just to keep 
things as clean as possible.

Best, Pratip

> Kipper Fletez-Brant <mailto:cafletezbrant at gmail.com>
> June 25, 2014 8:56 AM
> Hi Justin,
>
> We (Pratip and I) think it may likely be your data - we have observed 
> that the early time points of collection in a flow run tend to have 
> the most errors.  Pratip can speak a little more to the technical 
> causes of this.  We appreciate your comments and look forward to the 
> results of your tests.
>
> Kipper
>
>
> Hi Kipper,
>
> On second thought, I think it is my data. I just checked a few files 
> and they seem to be consistent with only removing the first 
> compartment. I will run some tests tomorrow to validate this. Sorry 
> for the emails.
>
> Thanks,
> Justin
>
> ________________________________________
> From: Justin Meskas
> Sent: June 24, 2014 4:31 PM
> To: Kipper Fletez-Brant
> Cc: Ryan Brinkman; bioconductor at r-project.org
> Subject: RE: flowClean
>
> Hi Kipper,
>
> Sorry to keep emailing you, but I had another question about 
> flowClean. I have been noticing that the clean function seems to label 
> the first compartment for removal every time. This seems odd to me. I 
> attached two figures. The figure called "A..." looks like most other 
> figures, where the first compartment is labelled for removal. And the 
> other figure, called "B...", is my unique case where, I believe 
> anyway, the first compartment should be removed, but not the second. 
> Are all these files somehow accidentally removing the first 
> compartment? Or do you think it is the case that all these files have 
> bad data at the beginning?
>
> Thank you,
> Justin