Dear all, I have gone through a number of steps in the analysis of 28 arrays of the Genomewide6.0 type and all seems OK until now:
#Fitting copy-number model and displaying results ####################################################################### ce <- ChromosomeExplorer(cbs) ce #ChromosomeExplorer: #Name: CLP #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY #Number of arrays: 28 #Path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs #RAM: 0.00MB process(ce, chromosomes=c (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23), verbose=verbose) And the end of the output after many hours run, looks like this: #20090610 02:17:03| Writing CN regions...done #20090610 02:17:03|Generating ChromosomeExplorer report...done #[1] TRUE #There were 50 or more warnings (use warnings() to see the first 50) I am looking at the 50 first warnings and I see that many are of the same type. here comes an example of one of the each category of warning. What shall I do now with each of those? 1: In library(package, lib.loc = lib.loc, character.only = TRUE, ... : there is no package called 'Cairo' 2: In method(static, ...) : Ghostscript not found. Searched directories: C:/gs, C:\Program/gs, / gs, C:\Program\Delade filer/gs 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : array has repeated maploc positions 4: In plotDev(pathname, width = width, height = height) : Unable to allocate bitmap 5: In plotDev(pathname, width = width, height = height) : opening device failed 6: In log(theta/thetaRef, base = 2) : NaNs produced 7: In log(theta * thetaRef, base = 2) : NaNs produced 8: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : array has repeated maploc positions Thanks a lot in adavnce for any help! Myriam --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
