[BioC] flowClean

[Justin Meskas]

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
________________________________________
From: Kipper Fletez-Brant [cafletezbrant at gmail.com]
Sent: June 23, 2014 4:38 PM
To: Justin Meskas
Cc: Ryan Brinkman; bioconductor at r-project.org
Subject: Re: flowClean

Great, thanks for the update!

On Mon 23 Jun 2014 05:26:21 PM EDT, Justin Meskas wrote:
> Hi Kipper,
>
> I downloaded your update and I ran "clean" on all my data for my current project and everything came out with no errors. Thank you very much for your quick fix.
>
> Justin
>
> ________________________________________
> From: Kipper Fletez-Brant [cafletezbrant at gmail.com]
> Sent: June 21, 2014 6:07 AM
> To: Justin Meskas
> Cc: Ryan Brinkman; bioconductor at r-project.org
> Subject: Re: flowClean
>
> Justin,
>
> Thanks for your patience.  I've fixed this and pushed an update to
> Bioconductor, which should be live tomorrow.
>
> Thanks again,
> Kipper
>
> On Thu 19 Jun 2014 06:41:04 PM EDT, Justin Meskas wrote:
>> Hi Kipper,
>>
>> Thank you for your quick reply. I had previously tried flowClean on uncompensated and untransformed data, and the same error was given.
>>
>> Thanks,
>> Justin
>>
>> ________________________________________
>> From: Kipper Fletez-Brant [cafletezbrant at gmail.com]
>> Sent: June 19, 2014 3:26 PM
>> To: Justin Meskas
>> Cc: Ryan Brinkman; bioconductor at r-project.org
>> Subject: Re: flowClean
>>
>> Hi Justin,
>>
>> I'm cc'ing the Bioc list so that others having this problem might see this.
>>
>> I have seen this error before. While it will take some time to diagnose, one comment I have is that we developed this algorithm to operate on uncompensated data. Try using flowClean before you do any other processing, and let me know how that works.
>>
>> Thanks,
>> Kipper
>>
>> On Jun 19, 2014 5:42 PM, "Justin Meskas" <jmeskas at bccrc.ca<mailto:jmeskas at bccrc.ca>> wrote:
>> Hello Kipper,
>>
>> I am in Dr. Ryan Brinkman's lab and I was trying to use your flowClean package. I have downloaded version 1.0.0 from Bioconductor and I received a similar error for many of my FCS files. I have attached one FCS file and the code I used to get the error. The error was the following:
>>
>> Error in if (x == 0) { : missing value where TRUE/FALSE needed
>>
>> I do not know if there is a problem with my data, or if I am using the data incorrectly with flowClean, but if there is any help you could provide me that would be greatly appreciated.
>>
>> Thank you,
>> Justin