DEXSeq- ExonCountSet
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@anitha-sundararajan-6152
Last seen 10.3 years ago
Hi I am a new user to DEXSeq and I was wondering if I could get some help resolving an error message I repeatedly get. I have my sample table and it looks like: > sampleTable countFile condition meiocyte1 Col-meiocyte-1.counts meiocytes meiocyte2 Col-meiocyte-2.counts meiocytes seedling1 Col-seedling-1.counts seedlings seedling2 Col-seedling-2.counts seedlings anther1 Col-anther-1.counts anthers anther2 Col-anther-2.counts anthers I am trying to create the ExonCountSet and I am constantly getting this error: > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, "Arabidopsis_thaliana.modified.flattened.gff") Error: could not find function "read.HTSeqCounts" I even tried newExonCountSet (read that in a blog) and that didn't work either! My session Info is as given: > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 Can you please give me any insight on what might be wrong. Thanks so much for your help in advance Anitha Sundararajan.
DEXSeq DEXSeq • 2.1k views
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@anitha-sundararajan-6152
Last seen 10.3 years ago
Hi I am a new user to DEXSeq and I was wondering if I could get some help resolving an error message I repeatedly get. I have my sample table and it looks like: > sampleTable countFile condition meiocyte1 Col-meiocyte-1.counts meiocytes meiocyte2 Col-meiocyte-2.counts meiocytes seedling1 Col-seedling-1.counts seedlings seedling2 Col-seedling-2.counts seedlings anther1 Col-anther-1.counts anthers anther2 Col-anther-2.counts anthers I am trying to create the ExonCountSet and I am constantly getting this error: > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, "Arabidopsis_thaliana.modified.flattened.gff") Error: could not find function "read.HTSeqCounts" I even tried newExonCountSet (read that in a blog) and that didn't work either! My session Info is as given: > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 Can you please give me any insight on what might be wrong. Thanks so much for your help in advance Anitha Sundararajan.
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Hi Anitha, You haven't loaded the DEXSeq package yet (note that it isn't listed in your sessionInfo() output). Best, Jim On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: > Hi > > I am a new user to DEXSeq and I was wondering if I could get some help > resolving an error message I repeatedly get. > > I have my sample table and it looks like: > > sampleTable > countFile condition > meiocyte1 Col-meiocyte-1.counts meiocytes > meiocyte2 Col-meiocyte-2.counts meiocytes > seedling1 Col-seedling-1.counts seedlings > seedling2 Col-seedling-2.counts seedlings > anther1 Col-anther-1.counts anthers > anther2 Col-anther-2.counts anthers > > I am trying to create the ExonCountSet and I am constantly getting > this error: > > > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > Error: could not find function "read.HTSeqCounts" > > I even tried newExonCountSet (read that in a blog) and that didn't > work either! > > My session Info is as given: > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 > > Can you please give me any insight on what might be wrong. > > Thanks so much for your help in advance > > Anitha Sundararajan. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Anitha, You haven't loaded the DEXSeq package yet (note that it isn't listed in your sessionInfo() output). Best, Jim On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: > Hi > > I am a new user to DEXSeq and I was wondering if I could get some help > resolving an error message I repeatedly get. > > I have my sample table and it looks like: > > sampleTable > countFile condition > meiocyte1 Col-meiocyte-1.counts meiocytes > meiocyte2 Col-meiocyte-2.counts meiocytes > seedling1 Col-seedling-1.counts seedlings > seedling2 Col-seedling-2.counts seedlings > anther1 Col-anther-1.counts anthers > anther2 Col-anther-2.counts anthers > > I am trying to create the ExonCountSet and I am constantly getting > this error: > > > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > Error: could not find function "read.HTSeqCounts" > > I even tried newExonCountSet (read that in a blog) and that didn't > work either! > > My session Info is as given: > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 > > Can you please give me any insight on what might be wrong. > > Thanks so much for your help in advance > > Anitha Sundararajan. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Thanks Jim! I should have noticed that. I had to import paths for R, gcc and other libs and re-load the package. That solved it. But I am running into another problem at the same step. When I run ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, "Arabidopsis_thaliana.modified.flattened.gff") I now get, Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : 'file' must be a character string or connection Can you please help me out with this error. Thanks again for your prompt response. Anitha On 4/10/14 11:23 AM, James W. MacDonald wrote: > Hi Anitha, > > You haven't loaded the DEXSeq package yet (note that it isn't listed > in your sessionInfo() output). > > Best, > > Jim > > > On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: >> Hi >> >> I am a new user to DEXSeq and I was wondering if I could get some >> help resolving an error message I repeatedly get. >> >> I have my sample table and it looks like: >> > sampleTable >> countFile condition >> meiocyte1 Col-meiocyte-1.counts meiocytes >> meiocyte2 Col-meiocyte-2.counts meiocytes >> seedling1 Col-seedling-1.counts seedlings >> seedling2 Col-seedling-2.counts seedlings >> anther1 Col-anther-1.counts anthers >> anther2 Col-anther-2.counts anthers >> >> I am trying to create the ExonCountSet and I am constantly getting >> this error: >> >> > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, >> "Arabidopsis_thaliana.modified.flattened.gff") >> Error: could not find function "read.HTSeqCounts" >> >> I even tried newExonCountSet (read that in a blog) and that didn't >> work either! >> >> My session Info is as given: >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 >> >> Can you please give me any insight on what might be wrong. >> >> Thanks so much for your help in advance >> >> Anitha Sundararajan. >> >> _______________________________________________ >> 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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Thanks Jim! I should have noticed that. I had to import paths for R, gcc and other libs and re-load the package. That solved it. But I am running into another problem at the same step. When I run ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, "Arabidopsis_thaliana.modified.flattened.gff") I now get, Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : 'file' must be a character string or connection Can you please help me out with this error. Thanks again for your prompt response. Anitha On 4/10/14 11:23 AM, James W. MacDonald wrote: > Hi Anitha, > > You haven't loaded the DEXSeq package yet (note that it isn't listed > in your sessionInfo() output). > > Best, > > Jim > > > On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: >> Hi >> >> I am a new user to DEXSeq and I was wondering if I could get some >> help resolving an error message I repeatedly get. >> >> I have my sample table and it looks like: >> > sampleTable >> countFile condition >> meiocyte1 Col-meiocyte-1.counts meiocytes >> meiocyte2 Col-meiocyte-2.counts meiocytes >> seedling1 Col-seedling-1.counts seedlings >> seedling2 Col-seedling-2.counts seedlings >> anther1 Col-anther-1.counts anthers >> anther2 Col-anther-2.counts anthers >> >> I am trying to create the ExonCountSet and I am constantly getting >> this error: >> >> > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, >> "Arabidopsis_thaliana.modified.flattened.gff") >> Error: could not find function "read.HTSeqCounts" >> >> I even tried newExonCountSet (read that in a blog) and that didn't >> work either! >> >> My session Info is as given: >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 >> >> Can you please give me any insight on what might be wrong. >> >> Thanks so much for your help in advance >> >> Anitha Sundararajan. >> >> _______________________________________________ >> 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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Hi, On Thu, Apr 10, 2014 at 11:01 AM, Anitha Sundararajan <asundara at="" ncgr.org=""> wrote: > Thanks Jim! > > I should have noticed that. I had to import paths for R, gcc and other libs > and re-load the package. That solved it. > > But I am running into another problem at the same step. > > When I run > ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > > I now get, > Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : > 'file' must be a character string or connection > > Can you please help me out with this error. The elements in sampleTable$countFile aren't proper paths to the files where the count data are stored. Try: R> file.exists(sampleTable$countFile) This is likely because you have a relative path encoded in `sampleTable$countFile` and it is incorrect given the directory R is running in (which is `getwd()`) Perhaps you can fix it by putting absolute file paths in `sampleTable$countFile` or starting R from a more appropriate directory. -steve -- Steve Lianoglou Computational Biologist Genentech
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Hi, On Thu, Apr 10, 2014 at 11:01 AM, Anitha Sundararajan <asundara at="" ncgr.org=""> wrote: > Thanks Jim! > > I should have noticed that. I had to import paths for R, gcc and other libs > and re-load the package. That solved it. > > But I am running into another problem at the same step. > > When I run > ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > > I now get, > Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : > 'file' must be a character string or connection > > Can you please help me out with this error. The elements in sampleTable$countFile aren't proper paths to the files where the count data are stored. Try: R> file.exists(sampleTable$countFile) This is likely because you have a relative path encoded in `sampleTable$countFile` and it is incorrect given the directory R is running in (which is `getwd()`) Perhaps you can fix it by putting absolute file paths in `sampleTable$countFile` or starting R from a more appropriate directory. -steve -- Steve Lianoglou Computational Biologist Genentech
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Hi Anitha, The best thing to do in instances like this is to look at the help page. As an example, for ?read.HTSeqCounts I get: Arguments countfiles A string vector containing the output files with the paths from dexseq_count.py. Which might be worded a bit better, but it seems clear to me that the expectation is that the argument is a string that tells the function where the output files are (and presumably these files will then be read into R). Best, Jim On Thursday, April 10, 2014 2:01:20 PM, Anitha Sundararajan wrote: > Thanks Jim! > > I should have noticed that. I had to import paths for R, gcc and > other libs and re-load the package. That solved it. > > But I am running into another problem at the same step. > > When I run > ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > > I now get, > Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : > 'file' must be a character string or connection > > Can you please help me out with this error. > > Thanks again for your prompt response. > > Anitha > > On 4/10/14 11:23 AM, James W. MacDonald wrote: >> Hi Anitha, >> >> You haven't loaded the DEXSeq package yet (note that it isn't listed >> in your sessionInfo() output). >> >> Best, >> >> Jim >> >> >> On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: >>> Hi >>> >>> I am a new user to DEXSeq and I was wondering if I could get some >>> help resolving an error message I repeatedly get. >>> >>> I have my sample table and it looks like: >>> > sampleTable >>> countFile condition >>> meiocyte1 Col-meiocyte-1.counts meiocytes >>> meiocyte2 Col-meiocyte-2.counts meiocytes >>> seedling1 Col-seedling-1.counts seedlings >>> seedling2 Col-seedling-2.counts seedlings >>> anther1 Col-anther-1.counts anthers >>> anther2 Col-anther-2.counts anthers >>> >>> I am trying to create the ExonCountSet and I am constantly getting >>> this error: >>> >>> > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, >>> "Arabidopsis_thaliana.modified.flattened.gff") >>> Error: could not find function "read.HTSeqCounts" >>> >>> I even tried newExonCountSet (read that in a blog) and that didn't >>> work either! >>> >>> My session Info is as given: >>> >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 >>> >>> loaded via a namespace (and not attached): >>> [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 >>> >>> Can you please give me any insight on what might be wrong. >>> >>> Thanks so much for your help in advance >>> >>> Anitha Sundararajan. >>> >>> _______________________________________________ >>> 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 >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Anitha, The best thing to do in instances like this is to look at the help page. As an example, for ?read.HTSeqCounts I get: Arguments countfiles A string vector containing the output files with the paths from dexseq_count.py. Which might be worded a bit better, but it seems clear to me that the expectation is that the argument is a string that tells the function where the output files are (and presumably these files will then be read into R). Best, Jim On Thursday, April 10, 2014 2:01:20 PM, Anitha Sundararajan wrote: > Thanks Jim! > > I should have noticed that. I had to import paths for R, gcc and > other libs and re-load the package. That solved it. > > But I am running into another problem at the same step. > > When I run > ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > > I now get, > Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : > 'file' must be a character string or connection > > Can you please help me out with this error. > > Thanks again for your prompt response. > > Anitha > > On 4/10/14 11:23 AM, James W. MacDonald wrote: >> Hi Anitha, >> >> You haven't loaded the DEXSeq package yet (note that it isn't listed >> in your sessionInfo() output). >> >> Best, >> >> Jim >> >> >> On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: >>> Hi >>> >>> I am a new user to DEXSeq and I was wondering if I could get some >>> help resolving an error message I repeatedly get. >>> >>> I have my sample table and it looks like: >>> > sampleTable >>> countFile condition >>> meiocyte1 Col-meiocyte-1.counts meiocytes >>> meiocyte2 Col-meiocyte-2.counts meiocytes >>> seedling1 Col-seedling-1.counts seedlings >>> seedling2 Col-seedling-2.counts seedlings >>> anther1 Col-anther-1.counts anthers >>> anther2 Col-anther-2.counts anthers >>> >>> I am trying to create the ExonCountSet and I am constantly getting >>> this error: >>> >>> > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, >>> "Arabidopsis_thaliana.modified.flattened.gff") >>> Error: could not find function "read.HTSeqCounts" >>> >>> I even tried newExonCountSet (read that in a blog) and that didn't >>> work either! >>> >>> My session Info is as given: >>> >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 >>> >>> loaded via a namespace (and not attached): >>> [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 >>> >>> Can you please give me any insight on what might be wrong. >>> >>> Thanks so much for your help in advance >>> >>> Anitha Sundararajan. >>> >>> _______________________________________________ >>> 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 >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hej Anitha! That error means that either 1) you have a typo in your filename or 2) the file is not in your current working directory. Use getwd() to lookup your current directory and dir() to list its content. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Street Lab Department of Plant Physiology Ume? Plant Science Center Tel: +46 90 786 7989 Email: nicolas.delhomme at umu.se SLU - Ume? universitet Ume? S-901 87 Sweden --------------------------------------------------------------- On 10 Apr 2014, at 15:01, Anitha Sundararajan <asundara at="" ncgr.org=""> wrote: > Thanks Jim! > > I should have noticed that. I had to import paths for R, gcc and other > libs and re-load the package. That solved it. > > But I am running into another problem at the same step. > > When I run > ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, > "Arabidopsis_thaliana.modified.flattened.gff") > > I now get, > Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : > 'file' must be a character string or connection > > Can you please help me out with this error. > > Thanks again for your prompt response. > > Anitha > > On 4/10/14 11:23 AM, James W. MacDonald wrote: >> Hi Anitha, >> >> You haven't loaded the DEXSeq package yet (note that it isn't listed >> in your sessionInfo() output). >> >> Best, >> >> Jim >> >> >> On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: >>> Hi >>> >>> I am a new user to DEXSeq and I was wondering if I could get some >>> help resolving an error message I repeatedly get. >>> >>> I have my sample table and it looks like: >>>> sampleTable >>> countFile condition >>> meiocyte1 Col-meiocyte-1.counts meiocytes >>> meiocyte2 Col-meiocyte-2.counts meiocytes >>> seedling1 Col-seedling-1.counts seedlings >>> seedling2 Col-seedling-2.counts seedlings >>> anther1 Col-anther-1.counts anthers >>> anther2 Col-anther-2.counts anthers >>> >>> I am trying to create the ExonCountSet and I am constantly getting >>> this error: >>> >>>> ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, >>> "Arabidopsis_thaliana.modified.flattened.gff") >>> Error: could not find function "read.HTSeqCounts" >>> >>> I even tried newExonCountSet (read that in a blog) and that didn't >>> work either! >>> >>> My session Info is as given: >>> >>>> sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 >>> >>> loaded via a namespace (and not attached): >>> [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 >>> >>> Can you please give me any insight on what might be wrong. >>> >>> Thanks so much for your help in advance >>> >>> Anitha Sundararajan. >>> >>> _______________________________________________ >>> 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 >> > > _______________________________________________ > 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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Thanks so much for your response(s) I went back a did a couple of things and looks like I now have the exon count set. So I was running R in the same directory as the file(s) location. I still went ahead and specified the complete path for each file and I still got the same error message. I then took a look at the help page (?read.HTSeqCounts) per Jim's suggestion and defined a design file additionally. That seemed to work. Please see my commands below (just for reference) sampleTable <- data.frame (row.names=c("meiocyte1", "meiocyte2", "seedling1", "seedling2", "anther1", "anther2"), countFile=c("/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq /Col-meiocyte-1.counts", "/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- meiocyte-2.counts", "/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- seedling-1.counts", "/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- seedling-2.counts", "/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- anther-1.counts", "/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- anther-2.counts"), condition= c("meiocytes", "meiocytes", "seedlings", "seedlings", "anthers", "anthers"),stringsAsFactors=FALSE,check.names=FALSE) > file.exists(sampleTable$countFile) [1] TRUE TRUE TRUE TRUE TRUE TRUE countFiles <- sampleTable$countFile design <- sampleTable[,-1] > ecs <- read.HTSeqCounts(countFiles, design, "/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Arabidopsis_ thaliana.modified.flattened.gff") > ecs ExonCountSet (storageMode: environment) assayData: 171805 features, 6 samples element names: counts protocolData: none phenoData sampleNames: /home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- meiocyte-1.counts /home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- meiocyte-2.counts ... /home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col- anther-2.counts (6 total) varLabels: sizeFactor condition countfiles varMetadata: labelDescription featureData featureNames: AT1G01010:E001 AT1G01010:E002 ... ATMG01410:E001 (171805 total) fvarLabels: geneID exonID ... transcripts (13 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: Thanks again for all your input. Hoping to run this through completion with few problems :) Anitha On 4/10/14 12:26 PM, Nicolas Delhomme wrote: > Hej Anitha! > > That error means that either 1) you have a typo in your filename or 2) the file is not in your current working directory. Use getwd() to lookup your current directory and dir() to list its content. > > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Street Lab > Department of Plant Physiology > Ume? Plant Science Center > > Tel: +46 90 786 7989 > Email: nicolas.delhomme at umu.se > SLU - Ume? universitet > Ume? S-901 87 Sweden > --------------------------------------------------------------- > > On 10 Apr 2014, at 15:01, Anitha Sundararajan <asundara at="" ncgr.org=""> wrote: > >> Thanks Jim! >> >> I should have noticed that. I had to import paths for R, gcc and other >> libs and re-load the package. That solved it. >> >> But I am running into another problem at the same step. >> >> When I run >> ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, >> "Arabidopsis_thaliana.modified.flattened.gff") >> >> I now get, >> Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : >> 'file' must be a character string or connection >> >> Can you please help me out with this error. >> >> Thanks again for your prompt response. >> >> Anitha >> >> On 4/10/14 11:23 AM, James W. MacDonald wrote: >>> Hi Anitha, >>> >>> You haven't loaded the DEXSeq package yet (note that it isn't listed >>> in your sessionInfo() output). >>> >>> Best, >>> >>> Jim >>> >>> >>> On 4/10/2014 1:14 PM, Anitha Sundararajan wrote: >>>> Hi >>>> >>>> I am a new user to DEXSeq and I was wondering if I could get some >>>> help resolving an error message I repeatedly get. >>>> >>>> I have my sample table and it looks like: >>>>> sampleTable >>>> countFile condition >>>> meiocyte1 Col-meiocyte-1.counts meiocytes >>>> meiocyte2 Col-meiocyte-2.counts meiocytes >>>> seedling1 Col-seedling-1.counts seedlings >>>> seedling2 Col-seedling-2.counts seedlings >>>> anther1 Col-anther-1.counts anthers >>>> anther2 Col-anther-2.counts anthers >>>> >>>> I am trying to create the ExonCountSet and I am constantly getting >>>> this error: >>>> >>>>> ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable, >>>> "Arabidopsis_thaliana.modified.flattened.gff") >>>> Error: could not find function "read.HTSeqCounts" >>>> >>>> I even tried newExonCountSet (read that in a blog) and that didn't >>>> work either! >>>> >>>> My session Info is as given: >>>> >>>>> sessionInfo() >>>> R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 >>>> >>>> Can you please give me any insight on what might be wrong. >>>> >>>> Thanks so much for your help in advance >>>> >>>> Anitha Sundararajan. >>>> >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> 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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