[BioC] flowCore: logicle transformation of flow cytometry data

Nishant Gopalakrishnan ngopalak at fhcrc.org
Tue Mar 17 21:27:39 CET 2009

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(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


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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