Re: [aroma.affymetrix] Error: could not find function process
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$byChipType(GenomeWideSNP_6.Full) print(ugp) UgpGenomeInformation: Name: GenomeWideSNP_6.Full Tags: na31,hg19,HB20110328 Full name: GenomeWideSNP_6.Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6.Full/GenomeWideSNP_6.Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB Chip type: GenomeWideSNP_6,Full Thanks in advance Uma On Sat, Mar 23, 2013 at 5:52 PM, Uma Shankavaram uma.shankava...@gmail.comwrote: Sorry, I guess I overlooked it. Many thanks for the help. Uma On Sat, Mar 23, 2013 at 5:45 PM, Henrik Bengtsson henrik.bengts...@aroma-project.org wrote: On Sat, Mar 23, 2013 at 2:41 PM, Uma Shankavaram uma.shankava...@gmail.com wrote: Yes, I found it at the aroma.affymetrix.org site under labs. https://docs.google.com/document/d/1P8zyjvzpKvW1Zquys3DHCXCkzaENqILrOz99uTWxppk/edit Thanks. Though, at bit before that it says/said: log - verbose - Arguments$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.1252LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1]
Re: [aroma.affymetrix] Error: could not find function process
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.1252LC_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_2.1.3R.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 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.
Re: [aroma.affymetrix] Error: could not find function process
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.1252LC_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_2.1.3R.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 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.
Re: [aroma.affymetrix] Error: could not find function process
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 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.1252LC_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_2.1.3R.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 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
Re: [aroma.affymetrix] Error: could not find function process
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.1252LC_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_2.1.3R.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 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
Re: [aroma.affymetrix] Error: could not find function process
Yes, I found it at the aroma.affymetrix.org site under labs. https://docs.google.com/document/d/1P8zyjvzpKvW1Zquys3DHCXCkzaENqILrOz99uTWxppk/edit 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.1252LC_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_2.1.3R.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 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
Re: [aroma.affymetrix] Error: could not find function process
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.1252LC_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_2.1.3R.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
