[BioC] flowCore: Prerequisites for norm2Filter?

[Byron Ellis]

>From the backtrace it looks like the problem is in the covMcd method
implemented by rrcov (which we merely use). Did you try using the
cov.rob method to see if you get a similar crash? You might also want
to check your rrcov version to see if a newer one is available from
CRAN.

On 8/11/07, M. Jankowski <mjankowski at gmail.com> wrote:
> Hi all,
>
> Thank you all for your previous help. I really appreciate your assistance!
>
> When I follow the HowTo I am able to apply the norm2Filter to the
>
> > fs <- read.flowSet(path = system.file("extdata", "compdata", "data", package = "flowCore"), name.keyword = "SAMPLE ID", phenoData = list(name = "SAMPLE ID", Filename = "$FIL"))
> > morphGate <- norm2Filter(filterId = "MorphologyGate", "FSC-H","SSC-H", scale = 2)
> > smaller <- Subset(fs, morphGate)
> >
>
> However, the same sequence applied to my own data (see below) results
> in a segfault. I can't figure out what I am doing wrong. Can anyone
> help me out?
>
> Thanks!
> Matt
>
> > fs =  read.flowSet(path="/home/mdj/data/NL10", patt="NL10\ control01.00*", alter.names=TRUE,phenoData = list(name = "SAMPLE ID", Filename = "$FIL"))
> > morphGate <- norm2Filter(filterId = "MorphologyGate", "FSC.H","SSC.H", scale = 2)
> > smaller <- Subset(fs, morphGate)
>
>  *** caught segfault ***
> address 0xa74e000, cause 'memory not mapped'
>
> Traceback:
>  1: .Fortran("rffastmcd", x, n, p, quan, nsamp, initcovariance =
> initcov,     initmean = initmean, best = inbest, mcdestimate = deter,
>    weights = weights, exactfit = fit, coeff = plane, kount = kount,
>  adjustcov = adcov, seed, temp, index1, index2, nmahad, ndist,     am,
> am2, slutn, med, mad, sd, means, bmeans, w, fv1, fv2,     rec, sscp1,
> cova1, corr1, cinv1, cova2, cinv2, z, cstock,     mstock, c1stock,
> m1stock, dath, cutoff, chimed, PACKAGE = "rrcov")
>  2: .fastmcd(x, quan, nsamp, seed)
>  3: covMcd(y)
>  4: switch(table at method, covMcd = {    if (nrow(y) > table at n)
> covMcd(y[sample(nrow(y), table at n), ])    else covMcd(y)}, cov.rob = {
>   cov.rob(y)}, stop("How did you get here?"))
>  5: x %in% subset
>  6: x %in% subset
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
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-- 
Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian