Question: affylmGUI segfault on "pd.ragene.1.0.st.v1"
10.9 years ago by
Harry Mangalam • 70
Harry Mangalam • 70 wrote:
Hi All, I've been trying to get affylmGUI to run on my laptop (3GB, Ubuntu 8.04, R as below: ===== > sessionInfo() R version 2.8.0 (2008-10-20) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages:  tools tcltk stats graphics grDevices utils datasets  methods base other attached packages:  affylmGUI_1.16.0 affy_1.16.0 preprocessCore_1.0.0  affyio_1.6.1 Biobase_2.2.1 limma_2.16.3 ===== The commands to start affylmGUI are: library("pd.ragene.1.0.st.v1") # the array set, from Matt Settles library("oligo") library("affylmGUI") affylmGUI() when I try to load data, whether my own (or the estrogen data set), it segfaults at the same place: After I select a working directory, and select the targets file (included below), [R churns for a few seconds], and give the new data set a name, I can see that the data is 'available' via the data tree in the left panel. At the point where I try to view the RNA targets via Menu -> RNA Targets -> RNA Targets, and release the mouse button, it segfaults, leaving the traceback: http://moo.nac.uci.edu/~hjm/affylmGUI.traceback As I said above, this is the case if it's my data or the estrogen data set. If I try to bypass that step and go direct to normalization (with my data), it will eventually emit the error that I don't have the correct CDF environment: ==== Error message ==== Error in getCdfInfo(object): Could not obtain CDF environment, problems encountered: Specified environment does not contain RaGene-1_0-st-v1 Library - package ragene10stv1cdf not installed. Data for package affy did not contain ragene10stv1cdf Bioconductor - ragene10stv1cdf not available ======================= This despite loading without error the correct (from Matt Settles) library beforehand. > library("pd.ragene.1.0.st.v1") Does the spelling variant muck it up? Best wishes, harry ==== targets.txt (whitespaces are TABS) ==== Name FileName Target AB.1 0908F-02_AB_1.CEL AB_Only AB.2 0908F-02_AB_2.CEL AB_Only AB.3 0908F-02_AB_3.CEL AB_Only CIQ.1 0908F-02_CIQ_1.CEL CIQ_Only CIQ.2 0908F-02_CIQ_2.CEL CIQ_Only CIQ.3 0908F-02_CIQ_3.CEL CIQ_Only CIQ+AB.1 0908F-02_CIQ_AB_1.CEL CIQ_AB_CoTreatment CIQ+AB.2 0908F-02_CIQ_AB_2.CEL CIQ_AB_CoTreatment CIQ+AB.3 0908F-02_CIQ_AB_3.CEL CIQ_AB_CoTreatment Untreated.1 0908F-02_Untreated_1.CEL CONTROL Untreated.2 0908F-02_Untreated_2.CEL CONTROL Untreated.3 0908F-02_Untreated_3.CEL CONTROL -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824-0084(o), 949 285-4487(c) --- Good judgment comes from experience; Experience comes from bad judgment. [F. Brooks.]
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