Dear Benilton,

Thank you for your reply. I tried crlmm package for normalizing and
estimating copy number for Affy SNP6.0 data. The data includes 74  CEL
files, it is a prostate cancer dataset downloaded from GEO sessioin id
GSE14996.  I ran crlmm, cnrma, snprma successfully, however,I failed at
running computeCopynumber, which gave me NA for all the results. I attached
the code, some output and sessionInfo() below. I read crlmm vignettes for
copy number, genotyping and downstream analysis from the following webpage:
http://bioconductor.org/packages/2.4/bioc/html/crlmm.html, however I still
couldn't figure out the problem. It would be greatly appreciated if you
could give me some hints.

Thank you very much,
Ashley

##################### R code, some output and sessionInfo
#############################
R> library(crlmm)
R> library(genomewidesnp6Crlmm)
R> celFiles <- list.celfiles()
R> outdir <- "/scratch/AshleyL/CEL_FILE"
R> gender <- rep(1,74) # 1 is male, 2 is female
R> if (!exists("crlmmResult")) {
    if (file.exists(file.path(outdir, "crlmmResult.rda"))) {
        load(file.path(outdir, "intensities.rda"))
        load(file.path(outdir, "crlmmResult.rda"))
        }
    else {
        crlmmResult <- crlmm(celFiles, gender=gender, save.it = TRUE,
intensityFile = file.path(outdir, "intensities.rda"))
        save(crlmmResult, file = file.path(outdir, "crlmmResult.rda"))
    }
}

R> # Quantile normalize the nonpolymorphic probes and save the results.
R> if (!exists("cnrmaResult")) {
    if (file.exists(file.path(outdir, "cnrmaResult.rda")))
    load(file.path(outdir, "cnrmaResult.rda"))
else {
    cnrmaResult <- cnrma(celFiles, cdfName = "genomewidesnp6")
    save(cnrmaResult, file = file.path(outdir, "cnrmaResult.rda"))
}
}

R> # Do snprma for quantile normalization and summarization of polymorphic
probes and save the results.
R> if (!exists("snprmaOutput")) {
    if (file.exists(file.path(outdir, "snprmaOutput.rda")))
    load(file.path(outdir, "snprmaOutput.rda"))
else {
snprmaOutput <- snprma(celFiles)
save(snprmaOutput, file=file.path(outdir,"snprmaOutput.rda"))
}
}

R> # Estimate copy number
R> A<- snprmaOutput[["A"]]
R> B<- snprmaOutput[["B"]]
R> genotypes <- crlmm:::calls(crlmmResult)
R> conf <- confs(crlmmResult)
R> gender <- crlmmResult$gender
R> SNR <- crlmmResult$SNR
R> NP <- cnrmaResult$NP
R> dts <- celDates(celFiles)
R> table(format(dts, "%d %b %Y"))
R> SNRmin <- 5
R> require(Biobase)
R> sns <- sampleNames(crlmmResult)
R> plate <- substr(basename(sns), 74, 74)
R> plate <- basename(sns)
R> table(plate)
R> table(format(dts, "%d %b %Y"), plate)
R> if (!exists("env")) {
        if (!file.exists(file.path(outdir, paste("env_chr", CHR, ".rda", sep
= "")))) {
        env <- new.env()
        CHR <- 23
        computeCopynumber(chrom = CHR, A = A,
        B = B, calls = genotypes, conf = conf,
        NP = NP, plate = plate, envir = env,
        DF.PRIOR = 50, MIN.OBS = 1, SNR = SNR,bias.adj=TRUE,
        gender=gender, SNRmin = SNRmin)
        save(env, file = file.path(outdir, paste("env_chr",
        CHR, ".rda", sep = "")))
}
        else {
                load(file.path(outdir, paste("env_chr", CHR, ".rda", sep =
"")))
        }
}

R> require(oligoClasses)
R> path <- system.file("extdata", package = "genomewidesnp6Crlmm")
R> load(file.path(path, "snpProbes.rda"))
R> load(file.path(path, "cnProbes.rda"))
R> position <- snpProbes[match(env[["snps"]], rownames(snpProbes)),
        "position"]
R> position.np <- cnProbes[match(rownames(env[["NP"]]),
        rownames(cnProbes)), "position"]
R> CA <- env[["CA"]]
R> CB <- env[["CB"]]
R> snpCT <- CA + CB
R> npCT <- env[["CT"]]
R> CT <- rbind(snpCT, npCT)
R> dimnames(CT) <- list(c(env[["snps"]], rownames(env[["NP"]])),
        env[["sns"]])
 R> dim(A)
[1] 906600     74
R> dim(B)
[1] 906600     74
R> dim(NP)
[1] 937223     74
R> dim(CT)
[1] 86086    74
R> A[1:5,1:5]
     [,1] [,2] [,3] [,4] [,5]
[1,] 2810 2564 2588 3271 3346
[2,]  225  228  238  244  595
[3,] 1135  935 1055  821 1096
[4,]  504  486 1558  512  606
[5,] 1574 1756 1978 1797 1653
R> B[1:5,1:5]
     [,1] [,2] [,3] [,4] [,5]
[1,] 2424 2088 2484 3433 2991
[2,]  624  720  802  844  617
[3,] 4173 3479 3217 3221 3235
[4,] 2179 1904 1380 1786 1686
[5,]  344  391  420  409  333
R> NP[1:5,1:5]
          GSM374529.CEL GSM374530.CEL GSM374531.CEL GSM374532.CEL
GSM374533.CEL
CN_473963          1926          1769          1001           903
1253
CN_473964          5502          5657          4295          3041
4961
CN_473965          4274          3457          2812          1822
3042
CN_477984          4175          3931          3538          2780
2280
CN_473981          1606          1571          1091           624
985
R> CT[1:5,1:5]
              GSM374529.CEL GSM374530.CEL GSM374531.CEL GSM374532.CEL
SNP_A-1998091            NA            NA            NA            NA
SNP_A-1998092            NA            NA            NA            NA
SNP_A-1998095            NA            NA            NA            NA
SNP_A-1998097            NA            NA            NA            NA
SNP_A-1998099            NA            NA            NA            NA
              GSM374533.CEL
SNP_A-1998091            NA
SNP_A-1998092            NA
SNP_A-1998095            NA
SNP_A-1998097            NA
SNP_A-1998099            NA

# Somehow, results from computeCopynumber are all NA.

R> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] oligoClasses_1.4.0        Biobase_2.2.2
[3] genomewidesnp6Crlmm_1.0.2 crlmm_1.2.4

loaded via a namespace (and not attached):
 [1] affyio_1.8.1         annotate_1.18.0      AnnotationDbi_1.4.3
 [4] DBI_0.2-4            genefilter_1.20.0    mvtnorm_0.9-4
 [7] preprocessCore_1.2.1 RSQLite_0.7-0        splines_2.8.1
[10] survival_2.34-1
>




On Fri, Aug 21, 2009 at 11:46 AM, Benilton Carvalho <bcarvalh@jhsph.edu>wrote:

> Dear Ashley,
>
> you didn't provide your sessionInfo(). It's been a while we don't use
> BufferedMatrix in oligo, so I'm guessing you need to update oligo.
>
> For genotyping SNP 6.0 chips, this is not the recommended workflow.
>
> A) Using oligo, you should follow the vignette:
>
>
> http://www.bioconductor.org/packages/2.4/bioc/vignettes/oligo/inst/doc/oligo.pdf
>
> ie, pretty much:
>
> library(oligo)
> filenames <- list.celfiles()
> outputDir <- "someDirThatOligoWillCreateForYou"
> crlmm(filenames, outputDir)
>
> B) We have developed an enhanced version of oligo, implemented in the
> 'crlmm' package, in which case you're asked to follow:
>
>
> http://www.bioconductor.org/packages/2.4/bioc/vignettes/crlmm/inst/doc/genotyping.pdf
>
> HTH,
>
> b
>
>
> On Aug 21, 2009, at 1:15 PM, Ashley Lin wrote:
>
>  Dear all,
>>
>> I am trying to use oligo to analyze 75 Affy SNP6.0 chips. I have installed
>> BufferedMatrix, but when I do:
>>
>>  library(oligo)
>>> filenames<-dir(pattern="CEL$")
>>> rawData <- read.celfiles(filenames)
>>> preProcessedData <- snprma(rawData)
>>>
>>
>> It gave me an error message "Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "subBufferedMatrix", for
>> signature "matrix".
>>
>> What could be wrong?
>>
>> Thanks,
>> Ashley Lin
>>
>>       [[alternative HTML version deleted]]
>>
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>>
>
>

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