Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: ######################################################## library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = TRUE) BLData = readIllumina(arrayNames =NULL, useImages=TRUE, singleChannel=FALSE, backgroundMethod ="rma", annoPkg= NULL, metrics=FALSE, metricsFile="Metrics.txt", normalizeMethod="quantile", tiffExtGrn="_Grn.TIF", tiffExtRed="_Red.TIF") #################################################### After the above last command (4th one), I got this error message: #################################################### Found 96 arrays Error in order(dat1$ProbeID) : object 'dat1' not found In addition: Warning message: In readIllumina(arrayNames = NULL, useImages = TRUE, singleChannel = FALSE, : No annotation package was specified. Need to use SetAnnotation later ###################################################### I will appreciate help to troubleshoot this error. Thank you very much. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture, ARS National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: roger.vallejo@ars.usda.gov <mailto:roger.vallejo@ars.usda.gov> http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 <http: www.ars.usda.gov="" pandp="" people="" people.htm?personid="37662"> [[alternative HTML version deleted]]

Dear Roger, Error in order(dat1$ProbeID) : object 'dat1' not found it may be unable to scan your files, you should compile line by line the readIllimna program: if (useImages) { tifFiles = vector(length = length(arrays)) tifFiles = file.path(path, paste(arrays, tiffExtGrn, sep = "")) for (i in 1:k) { file = csv_files[i] if (csvNcol == 4) { fc = file(file, open = "r") dat1 = scan(file = fc, what = list(ProbeID = integer(0), NULL, GrnX = numeric(0), GrnY = numeric(0)), sep = sep, dec = dec, skip = 1, quiet = TRUE) close(fc) } else if (csvNcol == 7) { fc = file(file, open = "r") dat1 = scan(file = fc, what = list(ProbeID = integer(0), NULL, GrnX = numeric(0), GrnY = numeric(0), NULL, RedX = numeric(0), RedY = numeric(0)), sep = sep, dec = dec, skip = 1, quiet = TRUE) close(fc) } else if (csvNcol == 6) { fc = file(file, open = "r") dat1 = scan(file = fc, what = list(NULL, ProbeID = integer(0), NULL, NULL, GrnX = numeric(0), GrnY = numeric(0)), sep = sep, dec = dec, skip = 1, quiet = TRUE) close(fc) RedX = dat1$GrnX RedY = dat1$GrnY } * ord = order(dat1$ProbeID) /* error message*/* you have warning message because annoPkg option is NULL Best Regards Mohamed Vallejo, Roger a ?crit : > Dear R users, > > I am using the beadarray package. I am trying to upload raw bead- level > data using these commands: > > > > ######################################################## > > library(beadarray) > > > > datadir <- ("C:/Computer_programs/R/beadarray/cecilia") > > > > targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = > TRUE) > > > > BLData = readIllumina(arrayNames =NULL, useImages=TRUE, > singleChannel=FALSE, backgroundMethod ="rma", annoPkg= NULL, > metrics=FALSE, metricsFile="Metrics.txt", normalizeMethod="quantile", > tiffExtGrn="_Grn.TIF", tiffExtRed="_Red.TIF") > > #################################################### > > > > After the above last command (4th one), I got this error message: > > > > #################################################### > > Found 96 arrays > Error in order(dat1$ProbeID) : object 'dat1' not found > In addition: Warning message: > In readIllumina(arrayNames = NULL, useImages = TRUE, singleChannel = > FALSE, : > No annotation package was specified. Need to use SetAnnotation later > > ###################################################### > > > > I will appreciate help to troubleshoot this error. > > Thank you very much. > > Roger > > > > > > > > Roger L. Vallejo, Ph.D. > Computational Biologist & Geneticist > U.S. Department of Agriculture, ARS > National Center for Cool & Cold Water Aquaculture > 11861 Leetown Road > Kearneysville, WV 25430 > Voice: (304) 724-8340 Ext. 2141 > Email: roger.vallejo at ars.usda.gov <mailto:roger.vallejo at="" ars.usda.gov=""> > http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 > <http: www.ars.usda.gov="" pandp="" people="" people.htm?personid="37662"> > > > > > [[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 > > -- Mohamed Lajnef INSERM Unit? 955. 40 rue de Mesly. 94000 Cr?teil. Courriel : Mohamed.lajnef at inserm.fr tel. : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81 30 99