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Question: Beadarray readBeadSummaryData() problem
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gravatar for affy snp
9.2 years ago by
affy snp640
affy snp640 wrote:
Hi all, I am using beadarray R package to analyze illumina array data and have a problem with readBeadSummaryData(). > BSData = readBeadSummaryData(dataFile = dataFile) Error in readBeadSummaryData(dataFile = dataFile) : Could not find a column called ProbeID to use as bead identifiers. Check your file and try changing the 'ProbeID' and/or 'skip' arguments. The error said " Could not find a column called ProbeID to use... " but I do have such column in the dataFile. Can anyone familiar with beadarray package suggest how to get over this? Thanks a lot! Allen [[alternative HTML version deleted]]
ADD COMMENTlink modified 9.2 years ago by Diego F. Cortes10 • written 9.2 years ago by affy snp640
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gravatar for Sean Davis
9.2 years ago by
Sean Davis20k
United States
Sean Davis20k wrote:
On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp at="" gmail.com=""> wrote: > Hi all, > > I am using beadarray R package to analyze illumina array data and have a > problem > with readBeadSummaryData(). > >> BSData = readBeadSummaryData(dataFile = dataFile) > Error in readBeadSummaryData(dataFile = dataFile) : > Could not find a column called ProbeID to use as bead identifiers. Check > your file and try changing the 'ProbeID' and/or 'skip' arguments. > > The error said " Could not find a column called ProbeID to use... " but I do > have such column > in the dataFile. Can anyone familiar with beadarray package suggest how to > get over this? Hi, Allen. It will probably help to read the help for the readBeadSummaryData() function. You will need to look at the data file that you have and decide what column will represent the unique identifier for your arrays and assign that column name to the ProbeID argument. Also, if you do not have a few rows of header information, you may need to adjust the skip parameter. Since you say that you do have a ProbeID column, the skip parameter may be the thing to change. Sean
ADD COMMENTlink written 9.2 years ago by Sean Davis20k
Thank you, Sean. I will double check the help file. But, I do make the dataFile almost the same with the example file provided by beadarray package except that I have two columns in different order in my dataFile compared to the example file. I think 'skip parameter' is about to skip some header information (rows) and it should not matter with columns. Allen On Thu, Jun 12, 2008 at 5:04 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp@gmail.com> wrote: > > Hi all, > > > > I am using beadarray R package to analyze illumina array data and have a > > problem > > with readBeadSummaryData(). > > > >> BSData = readBeadSummaryData(dataFile = dataFile) > > Error in readBeadSummaryData(dataFile = dataFile) : > > Could not find a column called ProbeID to use as bead identifiers. > Check > > your file and try changing the 'ProbeID' and/or 'skip' arguments. > > > > The error said " Could not find a column called ProbeID to use... " but I > do > > have such column > > in the dataFile. Can anyone familiar with beadarray package suggest how > to > > get over this? > > Hi, Allen. It will probably help to read the help for the > readBeadSummaryData() function. You will need to look at the data > file that you have and decide what column will represent the unique > identifier for your arrays and assign that column name to the ProbeID > argument. Also, if you do not have a few rows of header information, > you may need to adjust the skip parameter. Since you say that you do > have a ProbeID column, the skip parameter may be the thing to change. > > Sean > [[alternative HTML version deleted]]
ADD REPLYlink written 9.2 years ago by affy snp640
On Thu, Jun 12, 2008 at 5:10 PM, ss <affysnp at="" gmail.com=""> wrote: > Thank you, Sean. I will double check the help file. But, I do > make the dataFile almost the same with the example file > provided by beadarray package except that I have two columns > in different order in my dataFile compared to the example file. > I think 'skip parameter' is about to skip some header information (rows) > and it should not matter with columns. The skip parameter does matter. How many rows are there before your column headings? The readBeadSummaryData assumes 8. Is that what you have? Sean > On Thu, Jun 12, 2008 at 5:04 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >> On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp at="" gmail.com=""> wrote: >> > Hi all, >> > >> > I am using beadarray R package to analyze illumina array data and have a >> > problem >> > with readBeadSummaryData(). >> > >> >> BSData = readBeadSummaryData(dataFile = dataFile) >> > Error in readBeadSummaryData(dataFile = dataFile) : >> > Could not find a column called ProbeID to use as bead identifiers. >> > Check >> > your file and try changing the 'ProbeID' and/or 'skip' arguments. >> > >> > The error said " Could not find a column called ProbeID to use... " but >> > I do >> > have such column >> > in the dataFile. Can anyone familiar with beadarray package suggest how >> > to >> > get over this? >> >> Hi, Allen. It will probably help to read the help for the >> readBeadSummaryData() function. You will need to look at the data >> file that you have and decide what column will represent the unique >> identifier for your arrays and assign that column name to the ProbeID >> argument. Also, if you do not have a few rows of header information, >> you may need to adjust the skip parameter. Since you say that you do >> have a ProbeID column, the skip parameter may be the thing to change. >> >> Sean > >
ADD REPLYlink written 9.2 years ago by Sean Davis20k
i see. thank you, sean. that should be the problem. i have none of header information. the real data right starts from the second row with the first row for column names. i appreciate! allen On 6/12/08, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Jun 12, 2008 at 5:10 PM, ss <affysnp at="" gmail.com=""> wrote: >> Thank you, Sean. I will double check the help file. But, I do >> make the dataFile almost the same with the example file >> provided by beadarray package except that I have two columns >> in different order in my dataFile compared to the example file. >> I think 'skip parameter' is about to skip some header information (rows) >> and it should not matter with columns. > > The skip parameter does matter. How many rows are there before your > column headings? The readBeadSummaryData assumes 8. Is that what you > have? > > Sean > >> On Thu, Jun 12, 2008 at 5:04 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>> >>> On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp at="" gmail.com=""> wrote: >>> > Hi all, >>> > >>> > I am using beadarray R package to analyze illumina array data and have >>> > a >>> > problem >>> > with readBeadSummaryData(). >>> > >>> >> BSData = readBeadSummaryData(dataFile = dataFile) >>> > Error in readBeadSummaryData(dataFile = dataFile) : >>> > Could not find a column called ProbeID to use as bead identifiers. >>> > Check >>> > your file and try changing the 'ProbeID' and/or 'skip' arguments. >>> > >>> > The error said " Could not find a column called ProbeID to use... " but >>> > I do >>> > have such column >>> > in the dataFile. Can anyone familiar with beadarray package suggest how >>> > to >>> > get over this? >>> >>> Hi, Allen. It will probably help to read the help for the >>> readBeadSummaryData() function. You will need to look at the data >>> file that you have and decide what column will represent the unique >>> identifier for your arrays and assign that column name to the ProbeID >>> argument. Also, if you do not have a few rows of header information, >>> you may need to adjust the skip parameter. Since you say that you do >>> have a ProbeID column, the skip parameter may be the thing to change. >>> >>> Sean >> >> >
ADD REPLYlink written 9.2 years ago by affy snp640
On Thu, Jun 12, 2008 at 5:28 PM, ss <affysnp at="" gmail.com=""> wrote: > i see. thank you, sean. that should be the problem. i have none of > header information. the real data right starts from the second row > with the first row for column names. i appreciate! allen Then, you will want skip=0. > On 6/12/08, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Thu, Jun 12, 2008 at 5:10 PM, ss <affysnp at="" gmail.com=""> wrote: >>> Thank you, Sean. I will double check the help file. But, I do >>> make the dataFile almost the same with the example file >>> provided by beadarray package except that I have two columns >>> in different order in my dataFile compared to the example file. >>> I think 'skip parameter' is about to skip some header information (rows) >>> and it should not matter with columns. >> >> The skip parameter does matter. How many rows are there before your >> column headings? The readBeadSummaryData assumes 8. Is that what you >> have? >> >> Sean >> >>> On Thu, Jun 12, 2008 at 5:04 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>> >>>> On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp at="" gmail.com=""> wrote: >>>> > Hi all, >>>> > >>>> > I am using beadarray R package to analyze illumina array data and have >>>> > a >>>> > problem >>>> > with readBeadSummaryData(). >>>> > >>>> >> BSData = readBeadSummaryData(dataFile = dataFile) >>>> > Error in readBeadSummaryData(dataFile = dataFile) : >>>> > Could not find a column called ProbeID to use as bead identifiers. >>>> > Check >>>> > your file and try changing the 'ProbeID' and/or 'skip' arguments. >>>> > >>>> > The error said " Could not find a column called ProbeID to use... " but >>>> > I do >>>> > have such column >>>> > in the dataFile. Can anyone familiar with beadarray package suggest how >>>> > to >>>> > get over this? >>>> >>>> Hi, Allen. It will probably help to read the help for the >>>> readBeadSummaryData() function. You will need to look at the data >>>> file that you have and decide what column will represent the unique >>>> identifier for your arrays and assign that column name to the ProbeID >>>> argument. Also, if you do not have a few rows of header information, >>>> you may need to adjust the skip parameter. Since you say that you do >>>> have a ProbeID column, the skip parameter may be the thing to change. >>>> >>>> Sean >>> >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 9.2 years ago by Sean Davis20k
Thank you, Sean. It works. Yeah, the default skip is 8. The Illumina array data we received from the in-house microarray facility include raw data without background correction and pre-processed data after background correction. Can you recommend which one is better suited for beadarray package? I heard people suggested with less-processed data but apparently beadarray did not encompass a function to do background correction. Thank-you! Allen On Thu, Jun 12, 2008 at 5:30 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, Jun 12, 2008 at 5:28 PM, ss <affysnp@gmail.com> wrote: > > i see. thank you, sean. that should be the problem. i have none of > > header information. the real data right starts from the second row > > with the first row for column names. i appreciate! allen > > Then, you will want skip=0. > > > On 6/12/08, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> On Thu, Jun 12, 2008 at 5:10 PM, ss <affysnp@gmail.com> wrote: > >>> Thank you, Sean. I will double check the help file. But, I do > >>> make the dataFile almost the same with the example file > >>> provided by beadarray package except that I have two columns > >>> in different order in my dataFile compared to the example file. > >>> I think 'skip parameter' is about to skip some header information > (rows) > >>> and it should not matter with columns. > >> > >> The skip parameter does matter. How many rows are there before your > >> column headings? The readBeadSummaryData assumes 8. Is that what you > >> have? > >> > >> Sean > >> > >>> On Thu, Jun 12, 2008 at 5:04 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > >>>> > >>>> On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp@gmail.com> wrote: > >>>> > Hi all, > >>>> > > >>>> > I am using beadarray R package to analyze illumina array data and > have > >>>> > a > >>>> > problem > >>>> > with readBeadSummaryData(). > >>>> > > >>>> >> BSData = readBeadSummaryData(dataFile = dataFile) > >>>> > Error in readBeadSummaryData(dataFile = dataFile) : > >>>> > Could not find a column called ProbeID to use as bead identifiers. > >>>> > Check > >>>> > your file and try changing the 'ProbeID' and/or 'skip' arguments. > >>>> > > >>>> > The error said " Could not find a column called ProbeID to use... " > but > >>>> > I do > >>>> > have such column > >>>> > in the dataFile. Can anyone familiar with beadarray package suggest > how > >>>> > to > >>>> > get over this? > >>>> > >>>> Hi, Allen. It will probably help to read the help for the > >>>> readBeadSummaryData() function. You will need to look at the data > >>>> file that you have and decide what column will represent the unique > >>>> identifier for your arrays and assign that column name to the ProbeID > >>>> argument. Also, if you do not have a few rows of header information, > >>>> you may need to adjust the skip parameter. Since you say that you do > >>>> have a ProbeID column, the skip parameter may be the thing to change. > >>>> > >>>> Sean > >>> > >>> > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]
ADD REPLYlink written 9.2 years ago by affy snp640
0
gravatar for Diego F. Cortes
9.2 years ago by
Diego F. Cortes10 wrote:
Dear All, I have installed R 2.6.2 in my Mac OSX 10.5.3, and when I tried to load Rgraphviz after succesful download and installation it returns the following error message: Loading required package: Rgraphviz Error in dyn.load(file, ...) : unable to load shared library '/Users/dfcortes/Library/R/2.6/ library/Rgraphviz/libs/i386/Rgraphviz.so': dlopen(/Users/dfcortes/Library/R/2.6/library/Rgraphviz/libs/i386/ Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib Referenced from: /Users/dfcortes/Library/R/2.6/library/Rgraphviz/ libs/i386/Rgraphviz.so Reason: image not found Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error in function () : library Rgraphviz could not be found ! If some one have had similar experience let me know how to get around that. Best, Diego ---------------------------------------------------------------------- ---------------------------------- Diego F. Cort?s, Ph.D. candidate Virginia Bioinformatics Institute Washington St. (MC 0447) Virginia Tech Blacksburg, VA 24061 USA Office: (540) 231-3218 Fax: (540) 231-2606 e-mail: dfcortes at vt.edu http://staff.vbi.vt.edu/dfcortes/ ---------------------------------------------------------------------- ----------------------------------- Message and signature (c)2006 Diego F. Cort?s All rights reserved ---------------------------------------------------------------------- ----------------------------------- On Jun 12, 2008, at 4:23 PM, ss wrote: > Hi all, > > I am using beadarray R package to analyze illumina array data and > have a > problem > with readBeadSummaryData(). > >> BSData = readBeadSummaryData(dataFile = dataFile) > Error in readBeadSummaryData(dataFile = dataFile) : > Could not find a column called ProbeID to use as bead identifiers. > Check > your file and try changing the 'ProbeID' and/or 'skip' arguments. > > The error said " Could not find a column called ProbeID to use... " > but I do > have such column > in the dataFile. Can anyone familiar with beadarray package suggest > how to > get over this? > > Thanks a lot! > > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.2 years ago by Diego F. Cortes10
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