XPS with Arabidopsis Gene 1.1 ST Array Strip
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Hi, I would like to analyse data from the Arabidopsis Gene 1.1 ST Array Strip with the XPS package. I created a scheme and tried to load some example data with with the function import.data(). This error message will appear: ------------------------- dataAll <- import.data(scheme.Ara, "AraGene1_1", celdir=celdir, celfiles=celfiles) Opening file </home> in <read> mode... Creating new file </home>... Importing </home> as <aragene_1_1_st_hybridization_rep_strip_1_a01.cel>... Error: Number of data groups is not 1! Error: CEL-file with version/magic number </home> is not supported. Fehler in import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = celfiles) : error in function ???ImportData??? Zus??tzlich: Warnmeldung: In import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = celfiles) : characters [](){}.:# etc in 'celnames' will be replaced with '_' ---------------------------- Does XPS support this kind of cel files? Regards, Benedikt -- output of sessionInfo(): sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xps_1.24.0 loaded via a namespace (and not attached): [1] tools_3.0.2 > traceback() Kein traceback vef??gbar -- Sent via the guest posting facility at bioconductor.org.
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.1 years ago
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Dear Benedikt, In principle, xps should support this array. Can you show me how you have created the scheme file 'scheme.Ara'? The code should be something like: scheme.aragene11st <- import.exon.scheme("aragene11st", filedir = file.path(scmdir, "na34"), file.path(libdir, "AraGene-1_1-st.clf"), file.path(libdir, "AraGene-1_1-st.pgf"), file.path(anndir, "Version14May", "AraGene-1_1-st-v1.na34.tair10.probeset.csv"), file.path(anndir, "Version14May", "AraGene-1_1-st-v1.na34.tair10.transcript.csv")) The error messages indicate that the CEL-files do not belong to the scheme or that they are in an unknown format. The GEO profile number for the Affymetrix AraGene-1_1-st array seems to be GPL17133. Sadly, there does not exist any data samples so that I cannot test this array. Thus could you please send me some CEL-files for this array so that I can test it. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 7/9/14 4:30 PM, Benedikt [guest] wrote: > Hi, > > I would like to analyse data from the Arabidopsis Gene 1.1 ST Array Strip with the XPS package. I created a scheme and tried to load some example data with with the function import.data(). This error message will appear: > > ------------------------- > dataAll <- import.data(scheme.Ara, "AraGene1_1", celdir=celdir, celfiles=celfiles) > Opening file </home> in <read> mode... > Creating new file </home>... > Importing </home> as <aragene_1_1_st_hybridization_rep_strip_1_a01.cel>... > Error: Number of data groups is not 1! > Error: CEL-file with version/magic number </home> is not supported. > Fehler in import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = celfiles) : > error in function ???ImportData??? > Zus??tzlich: Warnmeldung: > In import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = celfiles) : > characters [](){}.:# etc in 'celnames' will be replaced with '_' > ---------------------------- > > Does XPS support this kind of cel files? > > Regards, > > Benedikt > > -- output of sessionInfo(): > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.24.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.2 >> traceback() > Kein traceback vef??gbar > > -- > Sent via the guest posting facility at bioconductor.org. >
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Dear Benedikt, I have just downloaded from Affymetrix strip array data for the HuGene-1_1_st array and can confirm your error messages. This means that xps does currently only support plate array data but does not support strip array data for the same type of expression array. Best regards, Christian On 7/9/14 8:19 PM, cstrato wrote: > Dear Benedikt, > > In principle, xps should support this array. > > Can you show me how you have created the scheme file 'scheme.Ara'? The > code should be something like: > > scheme.aragene11st <- import.exon.scheme("aragene11st", filedir = > file.path(scmdir, "na34"), > file.path(libdir, "AraGene-1_1-st.clf"), > file.path(libdir, "AraGene-1_1-st.pgf"), > file.path(anndir, "Version14May", > "AraGene-1_1-st-v1.na34.tair10.probeset.csv"), > file.path(anndir, "Version14May", > "AraGene-1_1-st-v1.na34.tair10.transcript.csv")) > > The error messages indicate that the CEL-files do not belong to the > scheme or that they are in an unknown format. > > The GEO profile number for the Affymetrix AraGene-1_1-st array seems to > be GPL17133. Sadly, there does not exist any data samples so that I > cannot test this array. Thus could you please send me some CEL-files for > this array so that I can test it. > > Best regards, > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l: cstrato at aon.at > _._._._._._._._._._._._._._._._._._ > > > > > On 7/9/14 4:30 PM, Benedikt [guest] wrote: >> Hi, >> >> I would like to analyse data from the Arabidopsis Gene 1.1 ST Array >> Strip with the XPS package. I created a scheme and tried to load some >> example data with with the function import.data(). This error message >> will appear: >> >> ------------------------- >> dataAll <- import.data(scheme.Ara, "AraGene1_1", celdir=celdir, >> celfiles=celfiles) >> Opening file >> </home> >> in <read> mode... >> Creating new file >> </home>... >> Importing >> </home> >> as <aragene_1_1_st_hybridization_rep_strip_1_a01.cel>... >> Error: Number of data groups is not 1! >> Error: CEL-file with version/magic number >> </home> >> is not supported. >> Fehler in import.data(scheme.Ara, "AraGene1_1", celdir = celdir, >> celfiles = celfiles) : >> error in function ???ImportData??? >> Zus??tzlich: Warnmeldung: >> In import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = >> celfiles) : >> characters [](){}.:# etc in 'celnames' will be replaced with '_' >> ---------------------------- >> >> Does XPS support this kind of cel files? >> >> Regards, >> >> Benedikt >> >> -- output of sessionInfo(): >> >> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=de_DE.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=de_DE.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] xps_1.24.0 >> >> loaded via a namespace (and not attached): >> [1] tools_3.0.2 >>> traceback() >> Kein traceback vef??gbar >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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cstrato ★ 3.9k
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Last seen 6.1 years ago
Austria
Dear Benedikt, I am glad that you have found a way to solve the problem, i.e. using PowerTools apt-cel-convert. If you look at the site for the Affymetrix Calvin Generic Data File Format, see: http://www.jotternotes.com/R/affxparser/Affymetrix_200811-FileFormats/ generic.html you will see that for strip arrays more than one Data Group is allowed. For normal arrays and plate arrays there is always only one Data Group, and thus I did implement the C++ code only for one Data Group. For this reason you did get the error: Number of data groups is not 1! Best regards, Christian P.S.: I am cc to BioC as information for other users of xps. On 7/10/14 2:47 PM, Benedikt Athmer wrote: > Dear Christian, > > I circumvent this problem by converting the cel-files (using Affymetrix > PowerTools apt-cel-convert -f text -o text_outdir *.cel) to text-cel > files. XPS does now import the text-cel files. I downloaded some > examples files from the affymetrix > (http://www.affymetrix.com/catalog/prod530004/AFFY/Model-and- applied-research-organisms-Gene-1.1-ST-Array-Strips#1_3) > where you can also find the library and annotation files. I'm still > explore the xps-package, I will get in touch with you, if there is > another problem, > > Benedikt >
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