[BioC] iFlow error in opening FCS and LMD files
Wolfgang Huber
whuber at embl.de
Tue Aug 17 23:25:48 CEST 2010
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
>
>
More information about the Bioconductor
mailing list