Dear all, I am interested in identifying different chromosomal states (gain,loss..) in array CGH data. Therefore I want to use the aCGH package, but I run into some problems. (I have tested Version 1.04 (stable) and the developmental Version 1.0.6) Maybe I can get some hints on how to proceed.... a) when I try to impute missing values (impute.lowess) I get the following errors: >Error in if (kb >= chrominfo$centromere[chr]) median(vec[clones.info$Chrom == : > missing value where TRUE/FALSE needed and additional in warnings() I find: >1: calling par(new=) with no plot >2: Collapsing to unique x values in: approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) >3: Collapsing to unique x values in: approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) ... it just works fine if I remove all the NAs from my data...but for sure that?s not the way the function is supposed to work ;o) b) when I try to find the hmm.states (find.hmm.states) I get this errors: >hmm(ex.acgh) <- find.hmm.states(ex.acgh) >Error in solve.default(z$hessian) : system is computationally singular: reciprocal condition number = >9.65772e-017 In addition: There were 50 or more warnings (use warnings() to see the first 50) Error in >nlm(likel, p, hessian = TRUE, print.level = print.level, typsiz = typsiz, : > non-finite value supplied by nlm In addition: There were 50 or more warnings (use warnings() to >see the first 50) Error in nlm(likel, p, hessian = TRUE, print.level = print.level, typsiz = typsiz, : > non-finite value supplied by nlm In addition: There were 49 warnings (use warnings() to see >them) Error in solve.default(z$hessian) : system is computationally singular: reciprocal condition >number = 1.74131e-017 In addition: There were 50 or more warnings (use warnings() to see the first 50) >Error in nlm(likel, p, hessian = TRUE, print.level = print.level, typsiz = typsiz, : > non-finite value supplied by nlm In addition: There were 50 or more warnings (use warnings() to >see the first 50) Error in nlm(likel, p, hessian = TRUE, print.level = print.level, typsiz = typsiz, : > non-finite value supplied by nlm In addition: Warning messages: >1: NA/Inf replaced by maximum positive value >2: NA/Inf replaced by maximum positive value >3: NA/Inf replaced by maximum positive value Warning messages: >1: NA/Inf replaced by maximum positive value >2: NaNs produced in: sqrt(diag(cov)) >3: Coercing LHS to a list >4: Coercing LHS to a list >5: NA/Inf replaced by maximum positive value >6: NA/Inf replaced by maximum positive value >7: NaNs produced in: sqrt(diag(cov)) >8: NA/Inf replaced by maximum positive value >9: NA/Inf replaced by maximum positive value >10: NaNs produced in: sqrt(diag(cov)) Here I'm totally lost... c) when I try to run the demo I get these errors . >demo(?aCGH?) > demo(aCGH) > ---- ~~~~ >Type <return> to start : > if (dev.cur() <= 1) get(getOption("device"))() > opar <- par(ask = interactive() && (.Device %in% c("X11", > "GTK", "windows", "quartz"))) > datadir <- system.file("examples", package = "aCGH") > latest.mapping.file <- file.path(datadir, "human.clones.info.Jul03.csv") > ex.acgh <- aCGH.read.Sprocs(system(paste("ls -1", > file.path(datadir, "*.txt")), intern = TRUE), latest.mapping.file, > chrom.remove.threshold = 23) >Error in system(paste("ls -1", file.path(datadir, "*.txt")), intern = TRUE) : > ls not found I suggest to use the built-in dir() function from R. It should be system independent .. kind regards, Grischa --------------- Deutsches Krebsforschungszentrum ------------- Grischa T?dt Molecular Genetics (B060) room TP3 1.105 German Cancer Research Center phone ++49 (0)6221 42-4582 Im Neuenheimer Feld 580 fax ++49 (0)6221 42-4639 D-69120 Heidelberg email g.toedt@dkfz.de Germany