Question: Problem with justSNPRMA, library "oligo"
0
gravatar for alessio boattini
10.8 years ago by
alessio boattini30 wrote:
Dear All, I am working with Affymetrix Genome Wide Human SNP Array 6.0 data. While pre-processing the data with the justSNPRMA function (library "oligo"), I obtained the error described below. An analogous problem was reported there: http://article.gmane.org/gmane.science.biology.informatics.conductor/1 7495 but there was no answer. Any hint? Many thanks Alessio > library(oligo) ... > setwd("/home/alessio/Documents/martinelli") > fullFilenames=list.celfiles() > fullFilenames [1] "20081009_1_SNP6.CEL" > preProcData=justSNPRMA(fullFilenames) Reading CEL files. Normalizing to Hapmap. Summarizing. Error in justSNPRMA(fullFilenames) : INTEGER() can only be applied to a 'integer', not a 'NULL' > traceback() 2: .Call("rma_c_complete_copy", tmpExprs, tmpExprs, pnVec, length(unique(pnVec)), body(bg.dens), new.env(), FALSE, FALSE, as.integer(2), PACKAGE = "oligo") 1: justSNPRMA(fullFilenames) > sessionInfo() R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pd.genomewidesnp.6_0.4.2 oligo_1.6.0 oligoClasses_1.4.0 [4] affxparser_1.14.2 AnnotationDbi_1.4.2 preprocessCore_1.4.0 [7] RSQLite_0.7-1 DBI_0.2-4 Biobase_2.2.1 [10] vegan_1.15-1
snp hapmap • 612 views
ADD COMMENTlink modified 10.8 years ago • written 10.8 years ago by alessio boattini30
Answer: Problem with justSNPRMA, library "oligo"
0
gravatar for Henrik Bengtsson
10.8 years ago by
United States
Henrik Bengtsson2.4k wrote:
Hi, the SNPRMA preprocessing method requires two or more arrays. This is because the probe summarization is done using the (two-way RMA-style) log-additive model. /Henrik Benilton, would you mind adding a test asserting that at least two arrays are passed, otherwise giving an error? On Tue, Feb 10, 2009 at 5:58 AM, alessio boattini <alessio.boattini2 at="" unibo.it=""> wrote: > Dear All, > > I am working with Affymetrix Genome Wide Human SNP Array 6.0 data. > While pre-processing the data with the justSNPRMA function (library > "oligo"), I obtained the error described below. > An analogous problem was reported there: > http://article.gmane.org/gmane.science.biology.informatics.conductor /17495 > but there was no answer. > Any hint? > Many thanks > Alessio > >> library(oligo) > ... >> setwd("/home/alessio/Documents/martinelli") >> fullFilenames=list.celfiles() >> fullFilenames > [1] "20081009_1_SNP6.CEL" >> preProcData=justSNPRMA(fullFilenames) > Reading CEL files. > Normalizing to Hapmap. > Summarizing. > Error in justSNPRMA(fullFilenames) : > INTEGER() can only be applied to a 'integer', not a 'NULL' > >> traceback() > 2: .Call("rma_c_complete_copy", tmpExprs, tmpExprs, pnVec, > length(unique(pnVec)), > body(bg.dens), new.env(), FALSE, FALSE, as.integer(2), PACKAGE = > "oligo") > 1: justSNPRMA(fullFilenames) > >> sessionInfo() > R version 2.8.1 (2008-12-22) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets > [8] methods base > > other attached packages: > [1] pd.genomewidesnp.6_0.4.2 oligo_1.6.0 > oligoClasses_1.4.0 > [4] affxparser_1.14.2 AnnotationDbi_1.4.2 > preprocessCore_1.4.0 > [7] RSQLite_0.7-1 DBI_0.2-4 > Biobase_2.2.1 > [10] vegan_1.15-1 > > _______________________________________________ > 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 >
ADD COMMENTlink written 10.8 years ago by Henrik Bengtsson2.4k
... hem ... that's it! Thanks a lot! Alessio On Tue, 2009-02-10 at 07:43 -0800, Henrik Bengtsson wrote: > Hi, > > the SNPRMA preprocessing method requires two or more arrays. This is > because the probe summarization is done using the (two-way RMA- style) > log-additive model. > > /Henrik > > Benilton, would you mind adding a test asserting that at least two > arrays are passed, otherwise giving an error? > > > On Tue, Feb 10, 2009 at 5:58 AM, alessio boattini > <alessio.boattini2 at="" unibo.it=""> wrote: > > Dear All, > > > > I am working with Affymetrix Genome Wide Human SNP Array 6.0 data. > > While pre-processing the data with the justSNPRMA function (library > > "oligo"), I obtained the error described below. > > An analogous problem was reported there: > > http://article.gmane.org/gmane.science.biology.informatics.conduct or/17495 > > but there was no answer. > > Any hint? > > Many thanks > > Alessio > > > >> library(oligo) > > ... > >> setwd("/home/alessio/Documents/martinelli") > >> fullFilenames=list.celfiles() > >> fullFilenames > > [1] "20081009_1_SNP6.CEL" > >> preProcData=justSNPRMA(fullFilenames) > > Reading CEL files. > > Normalizing to Hapmap. > > Summarizing. > > Error in justSNPRMA(fullFilenames) : > > INTEGER() can only be applied to a 'integer', not a 'NULL' > > > >> traceback() > > 2: .Call("rma_c_complete_copy", tmpExprs, tmpExprs, pnVec, > > length(unique(pnVec)), > > body(bg.dens), new.env(), FALSE, FALSE, as.integer(2), PACKAGE = > > "oligo") > > 1: justSNPRMA(fullFilenames) > > > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > i686-pc-linux-gnu > > > > locale: > > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID ENTIFICATION=C > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils > > datasets > > [8] methods base > > > > other attached packages: > > [1] pd.genomewidesnp.6_0.4.2 oligo_1.6.0 > > oligoClasses_1.4.0 > > [4] affxparser_1.14.2 AnnotationDbi_1.4.2 > > preprocessCore_1.4.0 > > [7] RSQLite_0.7-1 DBI_0.2-4 > > Biobase_2.2.1 > > [10] vegan_1.15-1 > > > > _______________________________________________ > > 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 > >
ADD REPLYlink written 10.8 years ago by alessio boattini30
Answer: Problem with justSNPRMA, library "oligo"
0
gravatar for alessio boattini
10.8 years ago by
alessio boattini30 wrote:
Dear Benilton, I tried the crlmm function, but it returns a very similar error, as you can see below. I hope that this will be useful. Other suggestions? Thanks for your help, Alessio > crlmm(fullFilenames,outDir) Loading required package: pd.genomewidesnp.6 Normalization: 100.00 percent done. Genotyping: 000.00 percent done.Error in getGenotypeRegionParams(alleleA[index, ] - alleleB[index, ], : INTEGER() can only be applied to a 'integer', not a 'NULL' > traceback() 4: .Call("R_trimmed_stats", M + (initialcalls - 2) * f, as.integer(initialcalls), 0.025) 3: getGenotypeRegionParams(alleleA[index, ] - alleleB[index, ], initialCalls[index, ], fs[index, ], verbose = FALSE) 2: genotypeOne(filenames, outdir, batch_size = batch_size, balance = balance, minLLRforCalls = minLLRforCalls, recalibrate = recalibrate, verbose = verbose, pkgname = pkgname, reference = reference) 1: crlmm(fullFilenames, outDir) On Tue, 2009-02-10 at 12:13 -0200, Benilton Carvalho wrote: > Alessio, > > thanks for your report. I've identified the problem and already have a > solution for it. > > In the meantime, you could use crlmm() instead: > > library(oligo) > outDir = "tmp" ## this will be created by crlmm() > fullFilenames = list.celfiles("/home/alessio/Documents/martinelli", > full.names=TRUE) > crlmm(fullFilenames, outDir) > > and, if you want the summaries: > > alleleA = readSummaries("alleleA", outDir) > alleleB = readSummaries("alleleB", outDir) > > Let me know how it goes. > > b > > On Feb 10, 2009, at 11:58 AM, alessio boattini wrote: > > > Dear All, > > > > I am working with Affymetrix Genome Wide Human SNP Array 6.0 data. > > While pre-processing the data with the justSNPRMA function (library > > "oligo"), I obtained the error described below. > > An analogous problem was reported there: > > http://article.gmane.org/gmane.science.biology.informatics.conduct or/17495 > > but there was no answer. > > Any hint? > > Many thanks > > Alessio > > > >> library(oligo) > > ... > >> setwd("/home/alessio/Documents/martinelli") > >> fullFilenames=list.celfiles() > >> fullFilenames > > [1] "20081009_1_SNP6.CEL" > >> preProcData=justSNPRMA(fullFilenames) > > Reading CEL files. > > Normalizing to Hapmap. > > Summarizing. > > Error in justSNPRMA(fullFilenames) : > > INTEGER() can only be applied to a 'integer', not a 'NULL' > > > >> traceback() > > 2: .Call("rma_c_complete_copy", tmpExprs, tmpExprs, pnVec, > > length(unique(pnVec)), > > body(bg.dens), new.env(), FALSE, FALSE, as.integer(2), PACKAGE = > > "oligo") > > 1: justSNPRMA(fullFilenames) > > > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > i686-pc-linux-gnu > > > > locale: > > LC_CTYPE > > = > > en_GB > > .UTF > > -8 > > ;LC_NUMERIC > > = > > C > > ;LC_TIME > > = > > en_GB > > .UTF > > -8 > > ;LC_COLLATE > > = > > en_GB > > .UTF > > -8 > > ;LC_MONETARY > > = > > C > > ;LC_MESSAGES > > = > > en_GB > > .UTF > > -8 > > ;LC_PAPER > > = > > en_GB > > .UTF > > -8 > > ;LC_NAME > > = > > C > > ;LC_ADDRESS > > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils > > datasets > > [8] methods base > > > > other attached packages: > > [1] pd.genomewidesnp.6_0.4.2 oligo_1.6.0 > > oligoClasses_1.4.0 > > [4] affxparser_1.14.2 AnnotationDbi_1.4.2 > > preprocessCore_1.4.0 > > [7] RSQLite_0.7-1 DBI_0.2-4 > > Biobase_2.2.1 > > [10] vegan_1.15-1 > > > > _______________________________________________ > > 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 >
ADD COMMENTlink written 10.8 years ago by alessio boattini30
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