Loading data into AgiMicroRna
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Steve Taylor ▴ 280
@steve-taylor-2838
Last seen 8.3 years ago
Hi, I am trying to use the AgiMicroRna package on Linux but I get an error when trying to read in the Agilent files of my data. >dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file My targets file looks like FileName Treatment GErep US45102931_252182712973_S01_miRNA_107_Sep09_1_1_DNA10203-001.txt CON 1 US45102931_252182712973_S01_miRNA_107_Sep09_1_2_DNA10203-002.txt CON 1 US45102931_252182712973_S01_miRNA_107_Sep09_1_3_DNA10203-004.txt C1 2 US45102931_252182712973_S01_miRNA_107_Sep09_1_4_DNA10203-005.txt C1 2 US45102931_252182712973_S01_miRNA_107_Sep09_2_1_DNA10203-006.txt C1 2 US45102931_252182712973_S01_miRNA_107_Sep09_2_2_DNA10203-007.txt C2 3 US45102931_252182712973_S01_miRNA_107_Sep09_2_3_DNA10203-008.txt C2 3 US45102931_252182712973_S01_miRNA_107_Sep09_2_4_DNA10203-009.txt C2 3 US45102931_252182712974_S01_miRNA_107_Sep09_1_1_DNA10203-010.txt C3 4 US45102931_252182712974_S01_miRNA_107_Sep09_1_2_DNA10203-011.txt C3 4 US45102931_252182712974_S01_miRNA_107_Sep09_1_3_DNA10203-012.txt C3 4 The column headers for my Agilent files are: FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal gTotalProbeSignal gTotalProbeError gTotalGeneSignal gTotalGeneError gIsGeneDetected I notice in the readMicroRnaAFEfunction it is looking for chr_coord, gBGUsedgTotalGeneSignal and gTotalProbeSignalgMeanSignal which do not appear in the input files. Any thoughts how I can get the data to load? >sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.ISO-8859-1 LC_NUMERIC=C [3] LC_TIME=en_GB.ISO-8859-1 LC_COLLATE=en_GB.ISO-8859-1 [5] LC_MONETARY=C LC_MESSAGES=en_GB.ISO-8859-1 [7] LC_PAPER=en_GB.ISO-8859-1 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 [4] limma_3.4.3 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 Kind regards and thanks, Steve
AgiMicroRna AgiMicroRna • 1.2k views
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Neel Aluru ▴ 460
@neel-aluru-3760
Last seen 6.0 years ago
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Hi Steve, You can find the answer to this in the mailing list archives. Pedro answered this couple of times. Search the archives for AgiMicroRna and you will have the answer. Neel On Oct 11, 2010, at 8:48 AM, Stephen Taylor wrote: > Hi, > > I am trying to use the AgiMicroRna package on Linux but I get an error when trying to read in the Agilent files of my data. > > >dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) > Error in readGenericHeader(fullname, columns = columns, sep = sep) : > Specified column headings not found in file > > My targets file looks like > > FileName Treatment GErep > US45102931_252182712973_S01_miRNA_107_Sep09_1_1_DNA10203-001.txt CON 1 > US45102931_252182712973_S01_miRNA_107_Sep09_1_2_DNA10203-002.txt CON 1 > US45102931_252182712973_S01_miRNA_107_Sep09_1_3_DNA10203-004.txt C1 2 > US45102931_252182712973_S01_miRNA_107_Sep09_1_4_DNA10203-005.txt C1 2 > US45102931_252182712973_S01_miRNA_107_Sep09_2_1_DNA10203-006.txt C1 2 > US45102931_252182712973_S01_miRNA_107_Sep09_2_2_DNA10203-007.txt C2 3 > US45102931_252182712973_S01_miRNA_107_Sep09_2_3_DNA10203-008.txt C2 3 > US45102931_252182712973_S01_miRNA_107_Sep09_2_4_DNA10203-009.txt C2 3 > US45102931_252182712974_S01_miRNA_107_Sep09_1_1_DNA10203-010.txt C3 4 > US45102931_252182712974_S01_miRNA_107_Sep09_1_2_DNA10203-011.txt C3 4 > US45102931_252182712974_S01_miRNA_107_Sep09_1_3_DNA10203-012.txt C3 4 > > > The column headers for my Agilent files are: > > > FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal gTotalProbeSignal gTotalProbeError gTotalGeneSignal gTotalGeneError gIsGeneDetected > > > I notice in the readMicroRnaAFEfunction it is looking for chr_coord, gBGUsedgTotalGeneSignal and gTotalProbeSignalgMeanSignal which do not appear in the input files. > > Any thoughts how I can get the data to load? > > >sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.ISO-8859-1 LC_NUMERIC=C > [3] LC_TIME=en_GB.ISO-8859-1 LC_COLLATE=en_GB.ISO-8859-1 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.ISO-8859-1 > [7] LC_PAPER=en_GB.ISO-8859-1 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 > [4] limma_3.4.3 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 > > > Kind regards and thanks, > > Steve > > _______________________________________________ > 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 > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607
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Hi, > > You can find the answer to this in the mailing list archives. Pedro answered this couple of times. Search the archives for AgiMicroRna and you will have the answer. > Thanks. The solution seems to be: >If the data is extracted with the FE report set to 'Full' rather than 'Compact', then it reports the gMeanSignal and >gBGUsed (but not chr_coord). You can then follow the package using the amendments Pedro posted to get around not >having the chr_coord column. I have got the files via a third party who got the samples processed by a company and I am not sure I will be able to get them to set FE report to "Full". Is there another workaround? Thanks, Steve > Neel > > On Oct 11, 2010, at 8:48 AM, Stephen Taylor wrote: > >> Hi, >> >> I am trying to use the AgiMicroRna package on Linux but I get an error when trying to read in the Agilent files of my data. >> >>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >> Specified column headings not found in file >> >> My targets file looks like >> >> FileName Treatment GErep >> US45102931_252182712973_S01_miRNA_107_Sep09_1_1_DNA10203-001.txt CON 1 >> US45102931_252182712973_S01_miRNA_107_Sep09_1_2_DNA10203-002.txt CON 1 >> US45102931_252182712973_S01_miRNA_107_Sep09_1_3_DNA10203-004.txt C1 2 >> US45102931_252182712973_S01_miRNA_107_Sep09_1_4_DNA10203-005.txt C1 2 >> US45102931_252182712973_S01_miRNA_107_Sep09_2_1_DNA10203-006.txt C1 2 >> US45102931_252182712973_S01_miRNA_107_Sep09_2_2_DNA10203-007.txt C2 3 >> US45102931_252182712973_S01_miRNA_107_Sep09_2_3_DNA10203-008.txt C2 3 >> US45102931_252182712973_S01_miRNA_107_Sep09_2_4_DNA10203-009.txt C2 3 >> US45102931_252182712974_S01_miRNA_107_Sep09_1_1_DNA10203-010.txt C3 4 >> US45102931_252182712974_S01_miRNA_107_Sep09_1_2_DNA10203-011.txt C3 4 >> US45102931_252182712974_S01_miRNA_107_Sep09_1_3_DNA10203-012.txt C3 4 >> >> >> The column headers for my Agilent files are: >> >> >> FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal gTotalProbeSignal gTotalProbeError gTotalGeneSignal gTotalGeneError gIsGeneDetected >> >> >> I notice in the readMicroRnaAFEfunction it is looking for chr_coord, gBGUsedgTotalGeneSignal and gTotalProbeSignalgMeanSignal which do not appear in the input files. >> >> Any thoughts how I can get the data to load? >> >>> sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.ISO-8859-1 LC_NUMERIC=C >> [3] LC_TIME=en_GB.ISO-8859-1 LC_COLLATE=en_GB.ISO-8859-1 >> [5] LC_MONETARY=C LC_MESSAGES=en_GB.ISO-8859-1 >> [7] LC_PAPER=en_GB.ISO-8859-1 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 >> [4] limma_3.4.3 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.16.0 >> >> >> Kind regards and thanks, >> >> Steve >> >> _______________________________________________ >> 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 >> > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > >
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Hi Steve, I am copying the mail from Pedro to the mailing list. I am thinking if you can read the files using read.maimages function it should work. HTH Neel Hi Neel and Richard, Thanks for your patience. I have slitghtly modified some code in the package, basically related to the way read.maimages is used. I have eliminated the use of the “chr_coord” column in some of the output files which it was what it was causing problems. Before these changes are made effective in the library, please, try this temporal solution: dd=read.maimages(files=targets$FileName,source="agilent", columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", Rb="gMeanSignal", Gb="gProcessedSignal"), other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", probe_mappings="probe_mappings", BGKmd="gBGMedianSignal", BGKus="gBGUsed"), annotation = c( "ControlType", "ProbeName","GeneName"), verbose=TRUE,sep="\t",quote="") before doing anything else, please check first that you have “probe_mappings” in the fifth position of “dd$other” > names(dd$other)[5] [1] "probe_mappings" Then, change the name of “probe_mappings” to the name that AgiMicroRna uses for this variable: > names(dd$other)[5] = "chr_coord" Then, use the rest of the functions as usual: ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) ddPROC = filterMicroRna(ddTGS.rma, dd, control = TRUE, IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 50, limNEG = 25, makePLOT = FALSE, targets, verbose = TRUE) Please, let me know if you still have any problem. Thanks p.- On Oct 11, 2010, at 9:26 AM, Stephen Taylor wrote: > Hi, > >> >> You can find the answer to this in the mailing list archives. Pedro answered this couple of times. Search the archives for AgiMicroRna and you will have the answer. >> > > Thanks. The solution seems to be: > > >If the data is extracted with the FE report set to 'Full' rather than 'Compact', then it reports the gMeanSignal and >gBGUsed (but not chr_coord). You can then follow the package using the amendments Pedro posted to get around not >having the chr_coord column. > > > I have got the files via a third party who got the samples processed by a company and I am not sure I will be able to get them to set FE report to "Full". Is there another workaround? > > Thanks, > > Steve > > >> Neel >> >> On Oct 11, 2010, at 8:48 AM, Stephen Taylor wrote: >> >>> Hi, >>> >>> I am trying to use the AgiMicroRna package on Linux but I get an error when trying to read in the Agilent files of my data. >>> >>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >>> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >>> Specified column headings not found in file >>> >>> My targets file looks like >>> >>> FileName Treatment GErep >>> US45102931_252182712973_S01_miRNA_107_Sep09_1_1_DNA10203-001.txt CON 1 >>> US45102931_252182712973_S01_miRNA_107_Sep09_1_2_DNA10203-002.txt CON 1 >>> US45102931_252182712973_S01_miRNA_107_Sep09_1_3_DNA10203-004.txt C1 2 >>> US45102931_252182712973_S01_miRNA_107_Sep09_1_4_DNA10203-005.txt C1 2 >>> US45102931_252182712973_S01_miRNA_107_Sep09_2_1_DNA10203-006.txt C1 2 >>> US45102931_252182712973_S01_miRNA_107_Sep09_2_2_DNA10203-007.txt C2 3 >>> US45102931_252182712973_S01_miRNA_107_Sep09_2_3_DNA10203-008.txt C2 3 >>> US45102931_252182712973_S01_miRNA_107_Sep09_2_4_DNA10203-009.txt C2 3 >>> US45102931_252182712974_S01_miRNA_107_Sep09_1_1_DNA10203-010.txt C3 4 >>> US45102931_252182712974_S01_miRNA_107_Sep09_1_2_DNA10203-011.txt C3 4 >>> US45102931_252182712974_S01_miRNA_107_Sep09_1_3_DNA10203-012.txt C3 4 >>> >>> >>> The column headers for my Agilent files are: >>> >>> >>> FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal gTotalProbeSignal gTotalProbeError gTotalGeneSignal gTotalGeneError gIsGeneDetected >>> >>> >>> I notice in the readMicroRnaAFEfunction it is looking for chr_coord, gBGUsedgTotalGeneSignal and gTotalProbeSignalgMeanSignal which do not appear in the input files. >>> >>> Any thoughts how I can get the data to load? >>> >>>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_GB.ISO-8859-1 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.ISO-8859-1 LC_COLLATE=en_GB.ISO-8859-1 >>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.ISO-8859-1 >>> [7] LC_PAPER=en_GB.ISO-8859-1 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 >>> [4] limma_3.4.3 Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 >>> >>> >>> Kind regards and thanks, >>> >>> Steve >>> >>> _______________________________________________ >>> 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 >>> >> >> Neel Aluru >> Postdoctoral Scholar >> Biology Department >> Woods Hole Oceanographic Institution >> Woods Hole, MA 02543 >> USA >> 508-289-3607 >> >> >> > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607 [[alternative HTML version deleted]]
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Hi again, > > I am copying the mail from Pedro to the mailing list. I am thinking if > you can read the files using read.maimages function it should work. > I have loaded my data in AgiMicroRna using: dd=read.maimages(files=targets.micro$FileName,source="agilent", columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", Rb="gMedianSignal", Gb="gProcessedSignal"), other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", BGKmd="gBGMedianSignal"), annotation = c( "ControlType", "ProbeName"), verbose=TRUE,sep="\t",quote="") There was no Rb="gMeanSignal", but I assume this should be ok. Everything looked ok until I tried to normalize the data. > ddTGS = tgsMicroRna(dd.micro, half = TRUE, makePLOT = FALSE,verbose = FALSE) > ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = FALSE,makePLOTpost = FALSE, targets.micro, verbose = TRUE) Error in xy.coords(x, y) : 'x' and 'y' lengths differ I see this problem has come up before on the list: http://article.gmane.org/gmane.science.biology.informatics.conductor/3 1182/match=xy+coords+x+y+lengths+differ+agimicrorna But I was wondering if there is a solution for it? Apologies if I have missed something. Thanks, Steve
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