Question: Problem "Error: is.character(filenames) is not TRUE" in read.xysfiles (Oligo package)
0
gravatar for Tommaso Raffaello
5.6 years ago by
Tommaso Raffaello60 wrote:
Hi, I have problem in reading my .xys files using the function read.xysfiles in Oligo package (I have created my .xys based on my .pair files following instruction I found on [BioC]). Here is what I have done: >basename(xys) [1] "Drained_control_1.xys" "Drained_control_2.xys" "Drained_control_3.xys" [4] "Drained_infected_resist_1.xys" "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys" [7] "Drained_infected_suscep_1.xys" "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys" [10] "Drained_wounding_1.xys" "Drained_wounding_2.xys" "Drained_wounding_3.xys" >is.character(xys) [1] TRUE >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified) Error: is.character(filenames) is not TRUE >sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 oligo_1.26.2 [4] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.6 [7] oligoClasses_1.24.0 affxparser_1.34.2 RSQLite_0.11.4 [10] DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-11 codetools_0.2-8 ff_2.2-12 [6] foreach_1.4.1 GenomicRanges_1.14.4 iterators_1.0.6 preprocessCore_1.24.0 splines_3.0.2 [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 (I have previously created the annotation package "pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using "Drained_control_1.xys" as template with apparently no problems and I have installed it). Sorry if this is a stupid problem, I´m learning R and Bioconductor at the same time in these weeks but I couldn´t find info about this problem. Thanks for your help! Tommaso -- Tommaso Raffaello, PhD University of Helsinki Department of Forest Sciences Latokartanonkaari 7 PO Box 27 00014 Helsinki (Finland) Phone number: +358 504486086 email: tommaso.raffaello@helsinki.fi email: tommaso.raffaello@gmail.com [[alternative HTML version deleted]]
annotation oligo pdinfobuilder • 4.8k views
ADD COMMENTlink modified 5.6 years ago by James W. MacDonald51k • written 5.6 years ago by Tommaso Raffaello60
Answer: Problem "Error: is.character(filenames) is not TRUE" in read.xysfiles (Oligo pac
0
gravatar for James W. MacDonald
5.6 years ago by
United States
James W. MacDonald51k wrote:
Hi Tommaso, If you look at the arguments for read.xysfiles, the first argument is '...', in which case you can't do positional argument matching. In other words, you need to specify all arguments. Read.xysfiles(filenames=xys, <other args="">). Best, Jim On Apr 11, 2014 2:24 AM, "Tommaso Raffaello" <tommaso.raffaello@helsinki.fi> wrote: > Hi, > > I have problem in reading my .xys files using the function read.xysfiles > in Oligo package (I have created my .xys based on my .pair files > following instruction I found on [BioC]). > > Here is what I have done: > > >basename(xys) > [1] "Drained_control_1.xys" "Drained_control_2.xys" > "Drained_control_3.xys" > [4] "Drained_infected_resist_1.xys" "Drained_infected_resist_2.xys" > "Drained_infected_resist_3.xys" > [7] "Drained_infected_suscep_1.xys" "Drained_infected_suscep_2.xys" > "Drained_infected_suscep_3.xys" > [10] "Drained_wounding_1.xys" "Drained_wounding_2.xys" > "Drained_wounding_3.xys" > >is.character(xys) > [1] TRUE > >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified) > Error: is.character(filenames) is not TRUE > > >sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 > oligo_1.26.2 > [4] Biostrings_2.30.1 XVector_0.2.0 > IRanges_1.20.6 > [7] oligoClasses_1.24.0 affxparser_1.34.2 > RSQLite_0.11.4 > [10] DBI_0.2-7 Biobase_2.22.0 > BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-11 > codetools_0.2-8 ff_2.2-12 > [6] foreach_1.4.1 GenomicRanges_1.14.4 iterators_1.0.6 > preprocessCore_1.24.0 splines_3.0.2 > [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > > > > (I have previously created the annotation package > "pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using > "Drained_control_1.xys" as template with apparently no problems and I > have installed it). > > Sorry if this is a stupid problem, I´m learning R and Bioconductor at > the same time in these weeks but I couldn´t find info about this problem. > > Thanks for your help! > > Tommaso > > -- > Tommaso Raffaello, PhD > > University of Helsinki > Department of Forest Sciences > Latokartanonkaari 7 PO Box 27 > 00014 Helsinki (Finland) > > Phone number: +358 504486086 > email: tommaso.raffaello@helsinki.fi > email: tommaso.raffaello@gmail.com > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.6 years ago by James W. MacDonald51k
Hi, Thanks! However, I still have some problems. Please see below what I have done. Actually I have downloaded and installed the "maqcExpression4plex-package" to check the xys files examples and mine should be ok. What could the problem be? Thank you so much for your help! Tommaso >pine_samples<-read.xysfiles(filenames=xys, pkgname="pd.110224.pinus.fa.exp.modified", checkType=FALSE) Platform design info loaded. Checking designs for each XYS file... Error in smartReadXYS(filenames, sampleNames) : Can't find 'designname=' field. C:\HY-data\TORAFFAE\Microarray Pine experiments\Drained peat Pine array\Drained_pine_analysis_files/Drained_control_1.xys corrupted? >sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 oligo_1.26.6 [4] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.7 [7] oligoClasses_1.24.0 affxparser_1.34.2 RSQLite_0.11.4 [10] DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-12 codetools_0.2-8 ff_2.2-13 [6] foreach_1.4.2 GenomicRanges_1.14.4 iterators_1.0.7 preprocessCore_1.24.0 splines_3.0.2 [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 On 12/04/2014 02:49, James W. MacDonald wrote: > > Hi Tommaso, > > If you look at the arguments for read.xysfiles, the first argument is > '...', in which case you can't do positional argument matching. In > other words, you need to specify all arguments. > > Read.xysfiles(filenames=xys, <other args="">). > > Best, > > Jim > > On Apr 11, 2014 2:24 AM, "Tommaso Raffaello" > <tommaso.raffaello@helsinki.fi <mailto:tommaso.raffaello@helsinki.fi="">> > wrote: > > Hi, > > I have problem in reading my .xys files using the function > read.xysfiles > in Oligo package (I have created my .xys based on my .pair files > following instruction I found on [BioC]). > > Here is what I have done: > > >basename(xys) > [1] "Drained_control_1.xys" "Drained_control_2.xys" > "Drained_control_3.xys" > [4] "Drained_infected_resist_1.xys" > "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys" > [7] "Drained_infected_suscep_1.xys" > "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys" > [10] "Drained_wounding_1.xys" "Drained_wounding_2.xys" > "Drained_wounding_3.xys" > >is.character(xys) > [1] TRUE > >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified) > Error: is.character(filenames) is not TRUE > > >sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United > Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 > oligo_1.26.2 > [4] Biostrings_2.30.1 XVector_0.2.0 > IRanges_1.20.6 > [7] oligoClasses_1.24.0 affxparser_1.34.2 > RSQLite_0.11.4 > [10] DBI_0.2-7 Biobase_2.22.0 > BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-11 > codetools_0.2-8 ff_2.2-12 > [6] foreach_1.4.1 GenomicRanges_1.14.4 iterators_1.0.6 > preprocessCore_1.24.0 splines_3.0.2 > [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > > > > (I have previously created the annotation package > "pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using > "Drained_control_1.xys" as template with apparently no problems and I > have installed it). > > Sorry if this is a stupid problem, I´m learning R and Bioconductor at > the same time in these weeks but I couldn´t find info about this > problem. > > Thanks for your help! > > Tommaso > > -- > Tommaso Raffaello, PhD > > University of Helsinki > Department of Forest Sciences > Latokartanonkaari 7 PO Box 27 > 00014 Helsinki (Finland) > > Phone number: +358 504486086 > email: tommaso.raffaello@helsinki.fi > <mailto:tommaso.raffaello@helsinki.fi> > email: tommaso.raffaello@gmail.com > <mailto:tommaso.raffaello@gmail.com> > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tommaso Raffaello, PhD University of Helsinki Department of Forest Sciences Latokartanonkaari 7 PO Box 27 00014 Helsinki (Finland) Phone number: +358 504486086 email: tommaso.raffaello@helsinki.fi email: tommaso.raffaello@gmail.com [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by Tommaso Raffaello60
Hi Tommaso, On 4/15/2014 7:03 AM, Tommaso Raffaello wrote: > Hi, > > Thanks! However, I still have some problems. > > Please see below what I have done. Actually I have downloaded and > installed the "maqcExpression4plex-package" to check the xys files > examples and mine should be ok. > > What could the problem be? > > Thank you so much for your help! > > Tommaso > > >pine_samples<-read.xysfiles(filenames=xys, pkgname="pd.110224.pinus.fa.exp.modified", checkType=FALSE) > Platform design info loaded. > Checking designs for each XYS file... > Error in smartReadXYS(filenames, sampleNames) : > Can't find 'designname=' field. C:\HY-data\TORAFFAE\Microarray Pine experiments\Drained peat Pine array\Drained_pine_analysis_files/Drained_control_1.xys corrupted? This error could indicate one of two things. First, the obvious that the file is corrupted. This is probably less likely, and it is more likely that R can't actually find the file itself. Try replacing the backslashes with either doubled backslashes (e.g., C:\\HY-data\\TORAFFAE...) or forward slashes (e.g., C:/HY- data/TORAFFAE...) Best, Jim > > >sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 oligo_1.26.6 > [4] Biostrings_2.30.1 XVector_0.2.0 IRanges_1.20.7 > [7] oligoClasses_1.24.0 affxparser_1.34.2 RSQLite_0.11.4 > [10] DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-12 codetools_0.2-8 ff_2.2-13 > [6] foreach_1.4.2 GenomicRanges_1.14.4 iterators_1.0.7 preprocessCore_1.24.0 splines_3.0.2 > [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > On 12/04/2014 02:49, James W. MacDonald wrote: >> >> Hi Tommaso, >> >> If you look at the arguments for read.xysfiles, the first argument is >> '...', in which case you can't do positional argument matching. In >> other words, you need to specify all arguments. >> >> Read.xysfiles(filenames=xys, <other args="">). >> >> Best, >> >> Jim >> >> On Apr 11, 2014 2:24 AM, "Tommaso Raffaello" >> <tommaso.raffaello at="" helsinki.fi="">> <mailto:tommaso.raffaello at="" helsinki.fi="">> wrote: >> >> Hi, >> >> I have problem in reading my .xys files using the function >> read.xysfiles >> in Oligo package (I have created my .xys based on my .pair files >> following instruction I found on [BioC]). >> >> Here is what I have done: >> >> >basename(xys) >> [1] "Drained_control_1.xys" "Drained_control_2.xys" >> "Drained_control_3.xys" >> [4] "Drained_infected_resist_1.xys" >> "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys" >> [7] "Drained_infected_suscep_1.xys" >> "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys" >> [10] "Drained_wounding_1.xys" "Drained_wounding_2.xys" >> "Drained_wounding_3.xys" >> >is.character(xys) >> [1] TRUE >> >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified) >> Error: is.character(filenames) is not TRUE >> >> >sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 >> LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United >> Kingdom.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 >> oligo_1.26.2 >> [4] Biostrings_2.30.1 XVector_0.2.0 >> IRanges_1.20.6 >> [7] oligoClasses_1.24.0 affxparser_1.34.2 >> RSQLite_0.11.4 >> [10] DBI_0.2-7 Biobase_2.22.0 >> BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-11 >> codetools_0.2-8 ff_2.2-12 >> [6] foreach_1.4.1 GenomicRanges_1.14.4 iterators_1.0.6 >> preprocessCore_1.24.0 splines_3.0.2 >> [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 >> >> >> >> (I have previously created the annotation package >> "pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using >> "Drained_control_1.xys" as template with apparently no problems and I >> have installed it). >> >> Sorry if this is a stupid problem, I?m learning R and Bioconductor at >> the same time in these weeks but I couldn?t find info about this >> problem. >> >> Thanks for your help! >> >> Tommaso >> >> -- >> Tommaso Raffaello, PhD >> >> University of Helsinki >> Department of Forest Sciences >> Latokartanonkaari 7 PO Box 27 >> 00014 Helsinki (Finland) >> >> Phone number: +358 504486086 >> email: tommaso.raffaello at helsinki.fi >> <mailto:tommaso.raffaello at="" helsinki.fi=""> >> email: tommaso.raffaello at gmail.com >> <mailto:tommaso.raffaello at="" gmail.com=""> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Tommaso Raffaello, PhD > > University of Helsinki > Department of Forest Sciences > Latokartanonkaari 7 PO Box 27 > 00014 Helsinki (Finland) > > Phone number: +358 504486086 > email:tommaso.raffaello at helsinki.fi > email:tommaso.raffaello at gmail.com -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 5.6 years ago by James W. MacDonald51k
Hi, thanks I solved the problem. The .xys file header was missing. I copied it from the .pair files. Thanks! Tommaso On 15/04/2014 17:33, James W. MacDonald wrote: > Hi Tommaso, > > On 4/15/2014 7:03 AM, Tommaso Raffaello wrote: >> Hi, >> >> Thanks! However, I still have some problems. >> >> Please see below what I have done. Actually I have downloaded and >> installed the "maqcExpression4plex-package" to check the xys files >> examples and mine should be ok. >> >> What could the problem be? >> >> Thank you so much for your help! >> >> Tommaso >> >> >pine_samples<-read.xysfiles(filenames=xys, >> pkgname="pd.110224.pinus.fa.exp.modified", checkType=FALSE) >> Platform design info loaded. >> Checking designs for each XYS file... >> Error in smartReadXYS(filenames, sampleNames) : >> Can't find 'designname=' field. C:\HY-data\TORAFFAE\Microarray >> Pine experiments\Drained peat Pine >> array\Drained_pine_analysis_files/Drained_control_1.xys corrupted? > > This error could indicate one of two things. First, the obvious that > the file is corrupted. This is probably less likely, and it is more > likely that R can't actually find the file itself. Try replacing the > backslashes with either doubled backslashes (e.g., > C:\\HY-data\\TORAFFAE...) or forward slashes (e.g., > C:/HY-data/TORAFFAE...) > > Best, > > Jim > > >> >> >sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] pd.110224.pinus.fa.exp.modified_0.0.1 >> pdInfoBuilder_1.26.0 oligo_1.26.6 >> [4] Biostrings_2.30.1 XVector_0.2.0 >> IRanges_1.20.7 >> [7] oligoClasses_1.24.0 affxparser_1.34.2 >> RSQLite_0.11.4 >> [10] DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.30.0 BiocInstaller_1.12.0 >> bit_1.1-12 codetools_0.2-8 ff_2.2-13 >> [6] foreach_1.4.2 GenomicRanges_1.14.4 >> iterators_1.0.7 preprocessCore_1.24.0 splines_3.0.2 >> [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 >> On 12/04/2014 02:49, James W. MacDonald wrote: >>> >>> Hi Tommaso, >>> >>> If you look at the arguments for read.xysfiles, the first argument >>> is '...', in which case you can't do positional argument matching. >>> In other words, you need to specify all arguments. >>> >>> Read.xysfiles(filenames=xys, <other args="">). >>> >>> Best, >>> >>> Jim >>> >>> On Apr 11, 2014 2:24 AM, "Tommaso Raffaello" >>> <tommaso.raffaello at="" helsinki.fi="">>> <mailto:tommaso.raffaello at="" helsinki.fi="">> wrote: >>> >>> Hi, >>> >>> I have problem in reading my .xys files using the function >>> read.xysfiles >>> in Oligo package (I have created my .xys based on my .pair files >>> following instruction I found on [BioC]). >>> >>> Here is what I have done: >>> >>> >basename(xys) >>> [1] "Drained_control_1.xys" "Drained_control_2.xys" >>> "Drained_control_3.xys" >>> [4] "Drained_infected_resist_1.xys" >>> "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys" >>> [7] "Drained_infected_suscep_1.xys" >>> "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys" >>> [10] "Drained_wounding_1.xys" "Drained_wounding_2.xys" >>> "Drained_wounding_3.xys" >>> >is.character(xys) >>> [1] TRUE >>> >read.xysfiles(xys, pd.110224.pinus.fa.exp.modified) >>> Error: is.character(filenames) is not TRUE >>> >>> >sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United Kingdom.1252 >>> LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United >>> Kingdom.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0 >>> oligo_1.26.2 >>> [4] Biostrings_2.30.1 XVector_0.2.0 >>> IRanges_1.20.6 >>> [7] oligoClasses_1.24.0 affxparser_1.34.2 >>> RSQLite_0.11.4 >>> [10] DBI_0.2-7 Biobase_2.22.0 >>> BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.30.0 BiocInstaller_1.12.0 bit_1.1-11 >>> codetools_0.2-8 ff_2.2-12 >>> [6] foreach_1.4.1 GenomicRanges_1.14.4 iterators_1.0.6 >>> preprocessCore_1.24.0 splines_3.0.2 >>> [11] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 >>> >>> >>> >>> (I have previously created the annotation package >>> "pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using >>> "Drained_control_1.xys" as template with apparently no problems >>> and I >>> have installed it). >>> >>> Sorry if this is a stupid problem, I?m learning R and >>> Bioconductor at >>> the same time in these weeks but I couldn?t find info about this >>> problem. >>> >>> Thanks for your help! >>> >>> Tommaso >>> >>> -- >>> Tommaso Raffaello, PhD >>> >>> University of Helsinki >>> Department of Forest Sciences >>> Latokartanonkaari 7 PO Box 27 >>> 00014 Helsinki (Finland) >>> >>> Phone number: +358 504486086 >>> email: tommaso.raffaello at helsinki.fi >>> <mailto:tommaso.raffaello at="" helsinki.fi=""> >>> email: tommaso.raffaello at gmail.com >>> <mailto:tommaso.raffaello at="" gmail.com=""> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> Tommaso Raffaello, PhD >> >> University of Helsinki >> Department of Forest Sciences >> Latokartanonkaari 7 PO Box 27 >> 00014 Helsinki (Finland) >> >> Phone number: +358 504486086 >> email:tommaso.raffaello at helsinki.fi >> email:tommaso.raffaello at gmail.com > -- Tommaso Raffaello, PhD University of Helsinki Department of Forest Sciences Latokartanonkaari 7 PO Box 27 00014 Helsinki (Finland) Phone number: +358 504486086 email: tommaso.raffaello at helsinki.fi email: tommaso.raffaello at gmail.com
ADD REPLYlink written 5.6 years ago by Tommaso Raffaello60
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