[BioC] flowCore: modifying exprs of a flowFrame

[Valerie Obenchain]

Hi Ariful,

This looks like a bug. I've cc'd a couple of the authors.

Valerie


On 12/06/12 15:18, Ariful Azad wrote:
> Hello Everybody,
>
> This is my first post to this list, so please advise me if this is not a
> right place to post this question.
>
> I was trying to modify a flowFrame by accessing the raw data matrix
> obtained from exprs(). This operation, however, does not changes tthe
> parameters of the flowFrame ( can be found by pData(parameters(ff)) ).
> In particular I was unable to use operations such as filter at later stage
> if I directly modify exprs(). Please take a look at the following two
> methods of transformations. They are essentially doing the same
> transformation but I am getting error in subsequent analysis if I transform
> exprs(ff) directly without using transform function in flowCore.
>
> ##### first use direct transformation... error on the filter #########
>
>> ff = GvHD[[1,3:4]]
>> exprs(ff) = asinh(exprs(ff)/10000)
>> ff
> flowFrame object 's5a01'
> with 3420 cells and 2 observables:
>       name      desc range minRange maxRange
> $P3 FL1-H CD15 FITC  1024        1    10000
> $P4 FL2-H   CD45 PE  1024        1    10000
> 124 keywords are stored in the 'description' slot
>> summary(ff)
>              FL1-H    FL2-H
> Min.    0.0001000 0.000100
> 1st Qu. 0.0004621 0.003833
> Median  0.0017590 0.010840
> Mean    0.0841400 0.033600
> 3rd Qu. 0.1090000 0.053100
> Max.    0.8814000 0.825300
>> c1f<- curv1Filter(filterId="myCurv1Filter", x='FL2-H')
>> fres<- filter(ff, c1f)
> Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,
> :
>    missing value where TRUE/FALSE needed
> In addition: Warning messages:
> 1: In min(x[, id]) : no non-missing arguments to min; returning Inf
> 2: In max(x[, id]) : no non-missing arguments to max; returning -Inf
>
> ##### Now use transformation of flowCore. No error on the filter #########
>
>> ff = GvHD[[1,3:4]]
>> ff = transform(ff, `FL1-H`=asinh(`FL1-H`/10000),
> `FL2-H`=asinh(`FL2-H`/10000))
>> ff
> flowFrame object 's5a01'
> with 3420 cells and 2 observables:
>       name      desc range minRange  maxRange
> $P3 FL1-H CD15 FITC  1024    1e-04 0.8813736
> $P4 FL2-H   CD45 PE  1024    1e-04 0.8813736
> 128 keywords are stored in the 'description' slot
>> summary(ff)
>              FL1-H    FL2-H
> Min.    0.0001000 0.000100
> 1st Qu. 0.0004621 0.003833
> Median  0.0017590 0.010840
> Mean    0.0841400 0.033600
> 3rd Qu. 0.1090000 0.053100
> Max.    0.8814000 0.825300
>> c1f<- curv1Filter(filterId="myCurv1Filter", x='FL2-H')
>> fres<- filter(ff, c1f)
> #########################################
>
> I am looking for a way such that the first method does work. I wanted to
> transform on exprs() because it is faster .
>
> Thanks
>
> Ariful Azad
> PhD Student
> Purdue University
>
> 	[[alternative HTML version deleted]]
>
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