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