[BioC] flowCore: logicle transformation of flow cytometry data

[fhahne at fhcrc.org]

Hi Pyne, Nishant,
I think the R wrapper should coerce the input to numeric. Integer  
values aren't that uncommon in flow data, although in a flowFrame they  
will always be stored as floating points. To most R users the notion  
of data types is not that relevant (after all, R automatically coerces  
in most cases), and this seems to be one of the places where a  
slightly more intelligent software doesn't hurt.
Florian


Quoting Nishant Gopalakrishnan <ngopalak at fhcrc.org>:

> Hi Pyne
>
> Its giving you an error because, the C function implementing the logicle
> transform is doing some type checking to see if the data supplied to it
> is a real number.
> for example ,
> ltr=logicleTransform("logicle")
> ltr(c(1:10))  ## would give you an error as class(c(1:10)) is "integer"
>
> ltr(as.real(c(1:10))) ## would work as the input is a real number
>
> Nishant
>
> Saumyadipta Pyne wrote:
>> Hi,
>>
>> I am doing some simulations on flow experiments, and therefore the
>> data are just a plain numerical matrix of fake scatter and marker
>> readouts. Thus, the data are not read with read.FCS nor saved as
>> a flowFrame. Instead I save the matrix as a data frame (call it Ab).
>>
>> The data, generated by me, have all entries present and containing
>> integral (real) values. When I try to apply the logicle transformation
>> to the data, it shows the following error:
>>
>> > ltr=logicleTransform("logicle")
>> > transform(Ab, "logicle.Ab1"=ltr(Ab1))
>> > Error in ltr(Ab1) : Input must be real values.
>>
>> However I do not get any error with, say, truncateTransform.
>> Is there a domain of real values for which logicle is not defined?
>> Please let me know what I might be doing wrong above.
>>
>> Thanks.
>> -Pyne
>>
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