[BioC] flowCore read.FCS unable to read FlowJo demo data set

[Nishant Gopalakrishnan]

Hi Johannes,

This appears to be a problem in the read.FCS function. Your demo FCS
files are using a bit width of 9 to represent a parameter. So far we
haven’t encountered files using an odd number of bits to represent a
parameter. However this appears to be valid as per the FCS standards.

I will try to put in a fix for this over the next couple of days.

Nishant

On 08/16/2010 10:37 PM, Johannes Rainer wrote:
> dear mailing list,
>
> I tried to read the demo FCS files from FlowJo's basic tutorial (
> http://www.flowjo.com/home/tutorial.html) using the read.FCS function, but I
> always get the following error message:
>
>   
>> Test <- read.FCS( "Sample 2.fcs" )
>>     
> Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale,
>  :
>   Don't know how to deal with bitwidth 9
>
>
> I would be grateful for any suggestions, or some hints whether this is a
> problem in the function, or of the data files.
>
> bests, jo
>
> my sessionInfo:
>
>   
>> sessionInfo()
>>     
> R version 2.11.1 (2010-05-31)
> i386-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] flowCore_1.14.1    rrcov_1.0-01       pcaPP_1.8-1        mvtnorm_0.9-92
>
> [5] robustbase_0.5-0-1 Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] feature_1.2.4 graph_1.26.0  ks_1.6.13     MASS_7.3-6    stats4_2.11.1
>
>
>
>