Question: DESeq2
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6.2 years ago by
Guest User12k
Guest User12k wrote:
Hi All, I decided to give DESeq2 a shot but my progress has been limited due to this annoying error whenever I want to save my results. Please have a look. write.csv(res, file="AN_WFDEgenes.csv") Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class 'structure("DataFrame", package = "IRanges")' into a data.frame I don't know how to go about it. -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.0.2 RcppArmadillo_0.3.800.1 Rcpp_0.10.3 [4] GenomicRanges_1.10.7 IRanges_1.16.6 pasilla_0.2.15 [7] DESeq_1.10.1 lattice_0.20-10 locfit_1.5-9 [10] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationDbi_1.20.7 biomaRt_2.14.0 [4] DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0 [7] grid_2.15.2 hwriter_1.3 parallel_2.15.2 [10] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.2 [13] splines_2.15.2 statmod_1.4.17 stats4_2.15.2 [16] stringr_0.6.2 survival_2.36-14 tools_2.15.2 [19] XML_3.96-1.1 xtable_1.7-1 > -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 6.2 years ago by Michael Love23k • written 6.2 years ago by Guest User12k
Answer: DESeq2
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gravatar for Michael Love
6.2 years ago by
Michael Love23k
United States
Michael Love23k wrote:
hi Yemmy, There was a missing 'as.data.frame' in the vignette which I corrected in version 1.0.4. The 'res' object is a DataFrame which can be exported after conversion to a data.frame. so you should do: write.csv(as.data.frame(res), file="AN_WFDEgenes.csv") Also, since version 1.0.3, we decided to rename the package class to 'DESeqDataSet' to save keystrokes and compress some long function names. A global find/replace of 'DESeqSummarizedExperiment' should take care of any problems. Mike On Mon, Apr 15, 2013 at 4:16 PM, Yemmy [guest] <guest@bioconductor.org>wrote: > > Hi All, > > I decided to give DESeq2 a shot but my progress has been limited due to > this annoying error whenever I want to save my results. Please have a look. > > write.csv(res, file="AN_WFDEgenes.csv") > Error in as.data.frame.default(x[[i]], optional = TRUE) : > cannot coerce class 'structure("DataFrame", package = "IRanges")' into a > data.frame > > I don't know how to go about it. > > -- output of sessionInfo(): > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DESeq2_1.0.2 RcppArmadillo_0.3.800.1 Rcpp_0.10.3 > [4] GenomicRanges_1.10.7 IRanges_1.16.6 pasilla_0.2.15 > [7] DESeq_1.10.1 lattice_0.20-10 locfit_1.5-9 > [10] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] annotate_1.36.0 AnnotationDbi_1.20.7 biomaRt_2.14.0 > [4] DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0 > [7] grid_2.15.2 hwriter_1.3 parallel_2.15.2 > [10] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.2 > [13] splines_2.15.2 statmod_1.4.17 stats4_2.15.2 > [16] stringr_0.6.2 survival_2.36-14 tools_2.15.2 > [19] XML_3.96-1.1 xtable_1.7-1 > > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 6.2 years ago by Michael Love23k
On 04/15/2013 08:16 AM, Michael Love wrote: > hi Yemmy, > > There was a missing 'as.data.frame' in the vignette which I corrected in > version 1.0.4. The 'res' object is a DataFrame which can be exported after > conversion to a data.frame. > > so you should do: > > write.csv(as.data.frame(res), file="AN_WFDEgenes.csv") > > Also, since version 1.0.3, we decided to rename the package class to > 'DESeqDataSet' to save keystrokes and compress some long function names. A > global find/replace of 'DESeqSummarizedExperiment' should take care of any > problems. > > Mike > > > > On Mon, Apr 15, 2013 at 4:16 PM, Yemmy [guest] <guest at="" bioconductor.org="">wrote: > >> >> Hi All, >> >> I decided to give DESeq2 a shot but my progress has been limited due to >> this annoying error whenever I want to save my results. Please have a look. >> >> write.csv(res, file="AN_WFDEgenes.csv") >> Error in as.data.frame.default(x[[i]], optional = TRUE) : >> cannot coerce class 'structure("DataFrame", package = "IRanges")' into a >> data.frame >> >> I don't know how to go about it. >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-w64-mingw32/x64 (64-bit) DESeq2 is not available via biocLite until R-3.0.0. You should install R-3.0.0 and use source("http://bioconductor.org/biocLite.R") biocLite("DESeq2") to install Bioconductor (and other) packages. Using other approaches will eventually lead to tears, even if this is not the cause of your current problems. Martin >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] DESeq2_1.0.2 RcppArmadillo_0.3.800.1 Rcpp_0.10.3 >> [4] GenomicRanges_1.10.7 IRanges_1.16.6 pasilla_0.2.15 >> [7] DESeq_1.10.1 lattice_0.20-10 locfit_1.5-9 >> [10] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.36.0 AnnotationDbi_1.20.7 biomaRt_2.14.0 >> [4] DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0 >> [7] grid_2.15.2 hwriter_1.3 parallel_2.15.2 >> [10] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.2 >> [13] splines_2.15.2 statmod_1.4.17 stats4_2.15.2 >> [16] stringr_0.6.2 survival_2.36-14 tools_2.15.2 >> [19] XML_3.96-1.1 xtable_1.7-1 >>> >> >> -- >> 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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 6.2 years ago by Martin Morgan ♦♦ 23k
Thanks. ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> To: Michael Love <michaelisaiahlove@gmail.com> uctor@r-project.org" <bioconductor@r-project.org> Sent: Monday, April 15, 2013 11:21 AM Subject: Re: [BioC] DESeq2 On 04/15/2013 08:16 AM, Michael Love wrote: > hi Yemmy, > > There was a missing 'as.data.frame' in the vignette which I corrected in > version 1.0.4. The 'res' object is a DataFrame which can be exported after > conversion to a data.frame. > > so you should do: > > write.csv(as.data.frame(res), file="AN_WFDEgenes.csv") > > Also, since version 1.0.3, we decided to rename the package class to > 'DESeqDataSet' to save keystrokes and compress some long function names.  A > global find/replace of 'DESeqSummarizedExperiment' should take care of any > problems. > > Mike > > > > On Mon, Apr 15, 2013 at 4:16 PM, Yemmy [guest] <guest@bioconductor.org>wrote: > >> >> Hi All, >> >> I decided to give DESeq2 a shot but my progress has been limited due to >> this annoying error whenever I want to save my results. Please have a look. >> >> write.csv(res, file="AN_WFDEgenes.csv") >> Error in as.data.frame.default(x[[i]], optional = TRUE) : >>    cannot coerce class 'structure("DataFrame", package = "IRanges")' into a >> data.frame >> >> I don't know how to go about it. >> >>  -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-w64-mingw32/x64 (64-bit) DESeq2 is not available via biocLite until R-3.0.0. You should install R-3.0.0 and use   source("http://bioconductor.org/biocLite.R")   biocLite("DESeq2") to install Bioconductor (and other) packages. Using other approaches will eventually lead to tears, even if this is not the cause of your current problems. Martin >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats    graphics  grDevices utils    datasets  methods base >> >> other attached packages: >>  [1] DESeq2_1.0.2            RcppArmadillo_0.3.800.1 Rcpp_0.10.3 >>  [4] GenomicRanges_1.10.7    IRanges_1.16.6 pasilla_0.2.15 >>  [7] DESeq_1.10.1            lattice_0.20-10        locfit_1.5-9 >> [10] DEXSeq_1.4.0            Biobase_2.18.0 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >>  [1] annotate_1.36.0      AnnotationDbi_1.20.7 biomaRt_2.14.0 >>  [4] DBI_0.2-5            genefilter_1.40.0    geneplotter_1.36.0 >>  [7] grid_2.15.2          hwriter_1.3          parallel_2.15.2 >> [10] RColorBrewer_1.0-5  RCurl_1.95-4.1      RSQLite_0.11.2 >> [13] splines_2.15.2      statmod_1.4.17      stats4_2.15.2 >> [16] stringr_0.6.2        survival_2.36-14    tools_2.15.2 >> [19] XML_3.96-1.1        xtable_1.7-1 >>> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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]] > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 [[alternative HTML version deleted]]
ADD REPLYlink written 6.2 years ago by oyeyemi ajayi10
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