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:

>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: > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Byron Ellis (byron.ellis at gmail.com) "Oook" -- The Librarian

Byron, This (plus cleaning up my data a little bit) solved my problem. Thanks! Matt On 8/11/07, Byron Ellis <byron.ellis at="" gmail.com=""> wrote: > The function installed.packages() can give you that. For reference, my > (working) version of rrcov is 0.3-06. To upgrade your packages to > latest versions you can use update.packages() or install.packages() > manually to get the current CRAN version. > > To test the rob.cov versus covMcd set method="cov.rob" when specifying > your norm2Filter. > > On 8/11/07, M. Jankowski <mjankowski at="" gmail.com=""> wrote: > > On 8/11/07, Byron Ellis <byron.ellis at="" gmail.com=""> wrote: > > > 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. > > > > > My newbieness to R is showing. How would I set up a test to check the > > rrcov method? My other question is how do I do a version check for > > rrcov? I'm running the CRAN 2.5.1 versioin of R on Ubuntu...but don't > > know how to check for a package version. > > > > Thanks for your help! > > Matt > > > > > -- > Byron Ellis (byron.ellis at gmail.com) > "Oook" -- The Librarian >