Problems with aCGH package
0
0
Entering edit mode
@grischa-todt-812
Last seen 7.1 years ago
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
aCGH Genetics Cancer CGH impute aCGH aCGH Genetics Cancer CGH impute aCGH • 837 views
ADD COMMENT

Login before adding your answer.

Traffic: 319 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6