Hi Henrik, Can you help why I getting this error at copy number segmentation step ?
ce <- ChromosomeExplorer(cbs, zooms=2^(0:5)) process(ce, array=1:2, chromosomes=c(1,2,7,22), verbose=verbose) Error: Failed to located UGP files for one of the chip types (GenomeWideSNP_6.Full). By checking the information of ugp file, seems like the file is seen ok. > ugp <- UgpGenomeInformation$byChipType("GenomeWideSNP_6.Full") > print(ugp) UgpGenomeInformation: Name: GenomeWideSNP_6.Full Tags: na31,hg19,HB20110328 Full name: GenomeWideSNP_6.Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6.Full/GenomeWideSNP_6.Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB Chip type: GenomeWideSNP_6,Full Thanks in advance Uma On Sat, Mar 23, 2013 at 5:52 PM, Uma Shankavaram <uma.shankava...@gmail.com>wrote: > Sorry, I guess I overlooked it. Many thanks for the help. > > Uma > > > On Sat, Mar 23, 2013 at 5:45 PM, Henrik Bengtsson < > henrik.bengts...@aroma-project.org> wrote: > >> On Sat, Mar 23, 2013 at 2:41 PM, Uma Shankavaram >> <uma.shankava...@gmail.com> wrote: >> > Yes, I found it at the aroma.affymetrix.org site under labs. >> > >> > >> https://docs.google.com/document/d/1P8zyjvzpKvW1Zquys3DHCXCkzaENqILrOz99uTWxppk/edit >> >> Thanks. Though, at bit before that it says/said: >> >> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> >> I've changed 'log' to 'verbose', because that will always work. >> >> /H >> >> > >> > Thx >> > >> > Uma >> > >> > >> > On Sat, Mar 23, 2013 at 5:32 PM, Henrik Bengtsson >> > <henrik.bengts...@aroma-project.org> wrote: >> >> >> >> On Sat, Mar 23, 2013 at 2:29 PM, Uma Shankavaram >> >> <uma.shankava...@gmail.com> wrote: >> >> > Dear Henrik, >> >> > >> >> > Thanks for the prompt fix. I have re-installed the library from the >> >> > source("http://aroma-project.org/hbLite.R") >> >> > hbInstall("aroma.core") >> >> > >> >> > Yes, it is working now, but there is still a small glitch. >> >> > It is failing if I pass the verbose argument. >> >> > >> >> > e.g. >> >> > process(ae, verbose = log) >> >> > >> >> > gives an error: >> >> > at #01. process(ae, verbose = log) >> >> > - process() is in environment 'aroma.core' >> >> > >> >> > Error: Argument 'verbose' is not a vector: function >> >> >> >> So, here 'log' probably equals base::log. Use verbose=TRUE (default) >> >> or a (negative) value, e.g. verbose=-10 (verbose=-20 shows more). >> >> >> >> Is there an (online?) example showing "process(ae, verbose = log)" >> >> that needs to be corrected? >> >> >> >> /Henrik >> >> >> >> >> >> >>>>>>>>>>>>>>>>>>>>>> >> >> > However, without verbose argument, gets the result. >> >> > process(ae) >> >> > Color maps: sqrt,yellow >> >> > Chip type: GenomeWideSNP_6.Full >> >> > Samples: GSM557940, GSM557941, GSM557942 >> >> > Aliases: GSM557940, GSM557941, GSM557942 >> >> > Color maps: sqrt,yellow >> >> > Chip type: GenomeWideSNP_6.Full >> >> > Samples: GSM557940, GSM557941, GSM557942 >> >> > Aliases: GSM557940, GSM557941, GSM557942 >> >> > [1] FALSE >> >> > >> >> > >> >> > Uma >> >> > >> >> > On Sat, Mar 23, 2013 at 5:05 PM, Henrik Bengtsson >> >> > <henrik.bengts...@aroma-project.org> wrote: >> >> >> >> >> >> I've fixed this. Running. >> >> >> >> >> >> source("http://aroma-project.org/hbLite.R") >> >> >> hbInstall("aroma.core") >> >> >> >> >> >> should fix this (you'll get aroma.core v2.8.3). Please let me know >> if >> >> >> this solved your problem. >> >> >> >> >> >> /Henrik >> >> >> >> >> >> PS. The problem appears when installing the R-forge binary of >> >> >> aroma.core (which in turn is due to temporary updates in R.rsp, >> which >> >> >> [is too much to explain]). I *think* this would only hit people who >> >> >> have R-forge setup in their getOption("repos") or install directly >> >> >> from R-forge, so most people would not be affected by this. I've >> >> >> updated hbInstall() to never install from R-forge. FYI, don't >> install >> >> >> from R-forge, because that contains my non-official >> under-construction >> >> >> and non-tested updates. >> >> >> >> >> >> >> >> >> On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson >> >> >> <henrik.bengts...@gmail.com> wrote: >> >> >> > I can reproduce this - very odd. I'll investigate a fix it. In >> the >> >> >> > meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g. >> >> >> > >> >> >> > install.packages("aroma.core", repos="@CRAN@") >> >> >> > install.packages("aroma.affymetrix", repos="@CRAN@") >> >> >> > >> >> >> > (Add repos="@CRAN@" to make sure not to install from other >> >> >> > repositories.) >> >> >> > >> >> >> > Thanks for the report, >> >> >> > >> >> >> > Henrik >> >> >> > >> >> >> > On Sat, Mar 23, 2013 at 10:16 AM, Uma Shankavaram >> >> >> > <uma.shankava...@gmail.com> wrote: >> >> >> >> Hello, >> >> >> >> >> >> >> >> I am using aroma.affymetrix_2.8.2 package using Windows version >> of R >> >> >> >> to >> >> >> >> process 4 SNP6.0 cel files. >> >> >> >> I am getting an error when trying to use this function. >> >> >> >> >> >> >> >> e.g. >> >> >> >> ae <- ArrayExplorer(csR) >> >> >> >> setColorMaps(ae, "sqrt,yellow") >> >> >> >> process(ae, verbose = log) >> >> >> >> ... >> >> >> >> Error: could not find function "process" >> >> >> >> >> >> >> >> Can anyone know why there is a problem? >> >> >> >> >> >> >> >> My R session info is: >> >> >> >>> sessionInfo() >> >> >> >> R version 2.15.1 (2012-06-22) >> >> >> >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> >> >> >> >> >> >> locale: >> >> >> >> [1] LC_COLLATE=English_United States.1252 >> LC_CTYPE=English_United >> >> >> >> States.1252 LC_MONETARY=English_United States.1252 >> >> >> >> [4] LC_NUMERIC=C LC_TIME=English_United >> >> >> >> States.1252 >> >> >> >> >> >> >> >> attached base packages: >> >> >> >> [1] stats graphics grDevices utils datasets methods >> base >> >> >> >> >> >> >> >> other attached packages: >> >> >> >> [1] aroma.affymetrix_2.8.2 affxparser_1.30.2 >> aroma.apd_0.2.3 >> >> >> >> R.huge_0.4.2 aroma.light_1.24.0 >> >> >> >> [6] aroma.core_2.8.2 matrixStats_0.6.2 R.rsp_0.8.2 >> >> >> >> R.devices_2.1.3 R.cache_0.6.8 >> >> >> >> [11] R.filesets_2.0.1 R.utils_1.19.5 R.oo_1.13.0 >> >> >> >> R.methodsS3_1.4.2 >> >> >> >> >> >> >> >> loaded via a namespace (and not attached): >> >> >> >> [1] digest_0.6.3 PSCBS_0.30.0 tools_2.15.1 >> >> >> >> >> >> >> >> >> >> >> >> Thanks >> >> >> >> >> >> >> >> Uma >> >> >> >> >> >> >> >> -- >> >> >> >> -- >> >> >> >> 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 with website >> http://www.aroma-project.org/. >> >> >> >> To post to this group, send email to >> >> >> >> aroma-affymetrix@googlegroups.com >> >> >> >> To unsubscribe and other options, go to >> >> >> >> http://www.aroma-project.org/forum/ >> >> >> >> >> >> >> >> --- >> >> >> >> You received this message because you are subscribed to the >> Google >> >> >> >> Groups >> >> >> >> "aroma.affymetrix" 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are subscribed to the Google >> >> >> Groups >> >> >> "aroma.affymetrix" group. >> >> >> To unsubscribe from this group and stop receiving emails from it, >> send >> >> >> an >> >> >> email to aroma-affymetrix+unsubscr...@googlegroups.com. >> >> >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >> >> >> >> >> > >> >> > >> >> > >> >> > -- >> >> > Uma >> >> > >> >> > -- >> >> > -- >> >> > 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 with website http://www.aroma-project.org/. >> >> > To post to this group, send email to >> aroma-affymetrix@googlegroups.com >> >> > To unsubscribe and other options, go to >> >> > http://www.aroma-project.org/forum/ >> >> > >> >> > --- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "aroma.affymetrix" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> send >> >> > an >> >> > email to aroma-affymetrix+unsubscr...@googlegroups.com. >> >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> > >> >> > >> >> >> >> -- >> >> -- >> >> 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 with website http://www.aroma-project.org/. >> >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> >> To unsubscribe and other options, go to >> >> http://www.aroma-project.org/forum/ >> >> >> >> --- >> >> You received this message because you are subscribed to the Google >> Groups >> >> "aroma.affymetrix" group. >> >> To unsubscribe from this group and stop receiving emails from it, send >> an >> >> email to aroma-affymetrix+unsubscr...@googlegroups.com. >> >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >> >> > >> > >> > >> > -- >> > Uma >> > >> > -- >> > -- >> > 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 with website http://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ >> > >> > --- >> > You received this message because you are subscribed to the Google >> Groups >> > "aroma.affymetrix" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an >> > email to aroma-affymetrix+unsubscr...@googlegroups.com. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> -- >> -- >> 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 with website http://www.aroma-project.org/. >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ >> >> --- >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to aroma-affymetrix+unsubscr...@googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > > -- > Uma > -- Uma -- -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.