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Question: DEXSeq- ExonCountSet
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gravatar for Anitha Sundararajan
4.6 years ago by
Anitha Sundararajan140 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$countfile, sampleTable, "Arabidopsis_thaliana.modified.flattened.gff") Error: could not find function "read.HTSeqCounts" I even tried newExonCountSet (read that in a blog) and that didn't work either! My session Info is as given: > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] hwriter_1.3 stringr_0.6.2 tools_3.0.2 Can you please give me any insight on what might be wrong. Thanks so much for your help in advance Anitha Sundararajan.
ADD COMMENTlink written 4.6 years ago by Anitha Sundararajan140
0
gravatar for Anitha Sundararajan
4.6 years ago by
Anitha Sundararajan140 wrote:
Hi I am a new user to DEXSeq and I was wondering if I could get some help resolving an error message I repeatedly get. I have my sample table and it looks like: > sampleTable countFile condition meiocyte1 Col-meiocyte-1.counts meiocytes meiocyte2 Col-meiocyte-2.counts meiocytes seedling1 Col-seedling-1.counts seedlings seedling2 Col-seedling-2.counts seedlings anther1 Col-anther-1.counts anthers anther2 Col-anther-2.counts anthers I am trying to create the ExonCountSet and I am constantly getting this error: > ecs <- read.HTSeqCounts (sampleTable$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.
ADD COMMENTlink written 4.6 years ago by Anitha Sundararajan140
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
ADD REPLYlink written 4.6 years ago by James W. MacDonald48k
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
ADD REPLYlink written 4.6 years ago by James W. MacDonald48k
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 >
ADD REPLYlink written 4.6 years ago by Anitha Sundararajan140
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 >
ADD REPLYlink written 4.6 years ago by Anitha Sundararajan140
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$countFile` or starting R from a more appropriate directory. -steve -- Steve Lianoglou Computational Biologist Genentech
ADD REPLYlink written 4.6 years ago by Steve Lianoglou12k
Hi, On Thu, Apr 10, 2014 at 11:01 AM, Anitha Sundararajan <asundara at="" ncgr.org=""> wrote: > Thanks Jim! > > I should have noticed that. I had to import paths for R, gcc and other libs > and re-load the package. That solved it. > > But I am running into another problem at the same step. > > When I run > ecs <- read.HTSeqCounts(sampleTable$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
ADD REPLYlink written 4.6 years ago by Steve Lianoglou12k
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
ADD REPLYlink written 4.6 years ago by James W. MacDonald48k
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
ADD REPLYlink written 4.6 years ago by James W. MacDonald48k
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
ADD REPLYlink written 4.6 years ago by Nicolas Delhomme320
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
ADD REPLYlink written 4.6 years ago by Anitha Sundararajan140
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