[BioC] iFlow error in opening FCS and LMD files

[Wolfgang Huber]

Dear Anna

[sorry that this comment is only on form, not substance, but:]

Can you
- provide the output of "sessionInfo()" (to see whether your package 
versions match and are sufficiently up-to-date)
- demonstrate your problem on data files that are publicly visible 
(either by making some of yours so, by putting them on the web 
somewhere, or by finding public ones that produce the same error).

I think this would greatly help the people here to see what your problem 
might be.

	Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

On Aug/17/10 8:38 PM, Josef Spidlen wrote:
> Hi Anna,
> I just tried one of our LMD files and it seems fine with both, flowCore
> and flowViz. So I would hope some of the flowViz guys could provide more
> insight in terms of what could the problem be. Generally, I think it
> should be possible to use flow* Bioconductor packages for cell cycle
> analysis. Alternatively, there's commercial software that could be used.
> Sorry, I have no experience there. I think some people mentioned that
> they used tools from verity software house. The paid version of Cyflogic
> should also be able to that.
>
> Cheers,
> Josef
>
> On 10-08-17 11:21 AM, Anna Dvorkin wrote:
>> Hello Josef,
>> Thank you very much for the information!
>> Following your advice, I tried to use the flowCore package, and I was
>> able to load one of the files I have. It was loaded without any
>> problems. Following is the output:
>> library(flowCore)
>> x<- read.FCS('path to LMD file')
>> flowFrame object 'A0-5  015.LMD'
>> with 35117 cells and 6 observables:
>>         name    desc range minRange maxRange
>> $P1  FS LIN  FS LIN  1024 0.000000     1023
>> $P2  SS LIN  SS LIN  1024 0.000000     1023
>> $P3 FL3 LIN  PI LIN  1024 0.000000     1023
>> $P4     AUX PI PEAK  1024 0.000000     1023
>> $P5 FL3 LOG  PI LOG  1024 1.000922    10000
>> $P6    TIME    TIME  1024 0.000000     1023
>> 139 keywords are stored in the 'descripton' slot
>>> summary(x)
>>          FS LIN SS LIN FL3 LIN  AUX FL3 LOG   TIME
>> Min.       4.0    1.0    25.0   23   244.9   0.00
>> 1st Qu.  233.0  145.0   392.0  343  3851.0  22.00
>> Median   333.0  222.0   495.0  404  4866.0  52.00
>> Mean     402.6  284.8   584.1  449  5725.0  56.81
>> 3rd Qu.  509.0  352.0   795.0  531  7772.0  89.00
>> Max.    1023.0 1023.0  1023.0 1023 10000.0 134.00
>>
>> However, when I tried to visualize the data with the flowViz package,
>> after typing:
>> library(flowViz)
>> plot(x)
>> I get the following error:
>> Error in x at parameters$name<mailto:x at parameters$name>  :
>>    '.SigArgs' is shorter than '.SigLength' says it should be
>>
>> Actually, I am interested in analyzing cell cycle data, and I thought
>> that I would be able to do that with the iFlow or flowCore + flowViz
>> packages.
>> Is there another option that can be helpful for that?
>> Thank you in advance!
>> Regards,
>> Anna
>
>