[BioC] Beadarray package

[Mohamed Lajnef]

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 écrit :
> 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]]
>
> _______________________________________________
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>
>   


-- 
Mohamed Lajnef
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