simpleaffy segmentation fault
Entering edit mode
Last seen 9.1 years ago
Dear List, I am using simpleaffy's detection.p.val method to get the P values of my arrays. When I set tau value 10^-1 and 10^-2, I get segmentation fault.For Tau val ues less than 10^-3 onwards it works fine. Any pointer on this will be very helpful. many thanks Sucheta Following is my source code: ============================= Data <- ReadAffy(filenames=file) Calls <- detection.p.val(Data,tau = 1e-2, calls=FALSE, alpha1=0.05,alpha2=0.05) Error Message: ============== Getting probe level data... Computing p-values *** caught segfault *** address (nil), cause 'memory not mapped' Traceback: 1: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), as.chara cter(pns), as.integer(length(mms[, x])), as.double(tau), as.double(sat), dpv al = double(length(unique.pns)), length(unique.pns), PACKAGE = "simpleaffy") 2: FUN(1[[1]], ...) 3: lapply(X, FUN, ...) 4: sapply(1:length(pms[1, ]), function(x) { .C("DetectionPValue", as.double( pms[, x]), as.double(mms[, x]), as.character(pns), as.integer(length(mms [, x])), as.double(tau), as.double(sat), dpval = double( s)), length(unique.pns), PACKAGE = "simpleaffy")$dpval}) 5: detection.p.val(Data, tau = 0.01, calls = FALSE, alpha1 = 0.05, alpha2 = 0.05) aborting ... Sessioninfo() ============= R version 2.4.0 (2006-10-03) i686-pc-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=en_ US;LC_MESS AGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEA SUREMENT=e n_US;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: simpleaffy genefilter survival affy affyio Biobase "2.8.0" "1.12.0" "2.29" "1.12.1" "1.0.0" "1.12.2" -- Sucheta Tripathy, Ph.D. Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 web page: blog : quick ref: l
Survival probe genefilter affy affyio Survival probe genefilter affy affyio • 1.3k views
Entering edit mode
vlagani • 0
Last seen 8.4 years ago

Dear Sucheta,

I have experienced a very similar problem in the last few days. In my case, the segmentation fault is caused by the C function "pma" called by "DetectionPValue". Essentially, pma calculates the quantities:

  for(i =0; i < n; i++){   
    dv[i] =(pms[i] - mms[i]) / (pms[i] + mms[i]);

Whenever dv[i] is exactly equal to tau, the program halts in segmentation fault. I have not been able to solve the issue within the C code, however an easy fix is to set tau to a number that is not likely to exactly match any value in dv[i], for example

tau <- 0.014999943534321443532455

Hope this helps,


Vincenzo Lagani

PostDoc Researcher

Foundation for Research and Technology - Hellas

Heraklion, Crete, Greece


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