AgiMicroRna and readMicroRnaFE
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Paulo Nuin ▴ 200
@paulo-nuin-3012
Last seen 6.9 years ago
Canada
Hi everyone I'm trying to read Agilent miRNA data with AgiMicroRna and readMicroRnaFE, but I'm finding an error due to some different column names. My data has this info miRNA_105_Dec08 (Read Only) 21-Nov-2008 12:14 Agilent Technologies Scanner G2505C US45102857 and the error on the command dd.micro <- readMicroRnaAFE(targets.micro, verbose = T) is Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file I dug a bit and found that 3 columns are missing on the input files: chr_coord gBGUsed gMeanSignal My question: is there a workaround this? I don't see column headers that would be similar to the three missing. Can I just change some column names to the ones the function is expecting? Any help is appreciated. Thanks in advance Paulo Nuin
miRNA AgiMicroRna miRNA AgiMicroRna • 766 views
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@richard-friedman-513
Last seen 7.3 years ago
On Aug 28, 2010, at 12:31 PM, Paulo Nuin wrote: > Hi everyone > > I'm trying to read Agilent miRNA data with AgiMicroRna and > readMicroRnaFE, but I'm finding an error due to some different > column names. My data has this info > > miRNA_105_Dec08 (Read Only) 21-Nov-2008 12:14 Agilent Technologies > Scanner G2505C US45102857 > > and the error on the command > > dd.micro <- readMicroRnaAFE(targets.micro, verbose = T) > > is > > Error in readGenericHeader(fullname, columns = columns, sep = sep) : > Specified column headings not found in file > > I dug a bit and found that 3 columns are missing on the input files: > > chr_coord > gBGUsed > gMeanSignal > > My question: is there a workaround this? I don't see column headers > that would be similar to the three missing. Can I just change some > column names to the ones the function is expecting? > > Any help is appreciated. > > Thanks in advance > > Paulo Nuin > _______________________________________________ > 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 Paulo, I am not sure if this is exactly the same problem I had 2 months ago, but in case it is I reproduce Pedro Lopez Romero's reply ro my problem at that time. ###################################################################### ############### from: plopez at cnic.es Subject: Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. Date: June 21, 2010 5:04:25 AM EDT To: naluru at whoi.edu, bioconductor at stat.math.ethz.ch 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.- ###################################################################### ############# I hope this help, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, George Scithers
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