Question: Problems with oligo and pd.genomewidesnp.6
0
gravatar for Jeremy Silver
11.6 years ago by
Jeremy Silver10 wrote:
Hello, I'm trying to call genotypes from Affymetrix SNP 6.0 chips using the oligo package. I've run into a small problem, that I think may be due to the differences between the bioconductor package pd.genomewidesnp.6 and the other pd.*.* annotation packages. Details are below. Any ideas? Thanks, Jeremy ############################################### # here are the names of the .CEL files > fullFilenamesOrigCelFiles[1:5] [1] "rawData/tds2008/GenomeWideSNP_6/SNP001_01_M001A.CEL" [2] "rawData/tds2008/GenomeWideSNP_6/SNP001_02_M003A.CEL" [3] "rawData/tds2008/GenomeWideSNP_6/SNP001_03_M007A.CEL" [4] "rawData/tds2008/GenomeWideSNP_6/SNP001_04_M015A.CEL" [5] "rawData/tds2008/GenomeWideSNP_6/SNP001_06_M026A.CEL" # call justSNPRMA > snpRmaResults <- justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], + verbose = TRUE, + phenoData = NULL, + normalizeToHapmap = TRUE) Reading CEL files. Normalizing to Hapmap. Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file '', probable reason 'No such file or directory' > traceback() 3: readChar(con, 5L, useBytes = TRUE) 2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package = pkgname)) 1: justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], verbose = TRUE, phenoData = NULL, normalizeToHapmap = TRUE) > sessionInfo() R version 2.7.0 (2008-04-22) i686-pc-linux-gnu locale: C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pd.genomewidesnp.6_0.4.1 aroma.affymetrix_0.9.1 aroma.apd_0.1.3 [4] R.huge_0.1.5 digest_0.3.1 aroma.light_1.7.2 [7] R.rsp_0.3.4 R.cache_0.1.7 R.utils_1.0.2 [10] R.oo_1.4.3 R.methodsS3_1.0.1 oligo_1.4.0 [13] oligoClasses_1.2.0 affxparser_1.11.14 AnnotationDbi_1.2.1 [16] preprocessCore_1.1.9 RSQLite_0.6-8 DBI_0.2-4 [19] Biobase_1.99.10 # See if we can find the problem - the following three lines come from justSNPRMA > filenames <- fullFilenamesOrigCelFiles[1:5] > headdetails <- readCelHeader(filenames[1]) > pkgname <- cleanPlatformName(headdetails[["chiptype"]]) # The problematic line asks to load the following file.... > system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package = pkgname) [1] "" # ... which doesn't seem to exist. Here's the folder we're looking at > system.file("extdata", package = pkgname) [1] "$HOME/R/i686-pc-linux-gnu-library/2.7/pd.genomewidesnp.6/extdata" # ... and here are the files it contains > list.files(system.file("extdata", package = pkgname)) [1] "pd.genomewidesnp.6.sqlite" "seqMat.rda" Looks like we were trying to load a file called "pd.genomewidesnp.6Ref.rda" from this folder.
snp annotation hapmap • 687 views
ADD COMMENTlink modified 11.6 years ago by Vincent J. Carey, Jr.6.3k • written 11.6 years ago by Jeremy Silver10
Answer: Problems with oligo and pd.genomewidesnp.6
0
gravatar for Vincent J. Carey, Jr.
11.6 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
it is not easy to work with these chips but i am trying to reproduce. i see your oligoClasses seems a bit out of date. you might update it and try again. i will be working on this in the mean time and will let you know what i find. the only 6.0 test data that i have are in the bioc hapmapsnp6 package. are there others on the net that might help robustify our testing procedure? pointers appreciated. --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Fri, 23 May 2008, Jeremy Silver wrote: > Hello, > > I'm trying to call genotypes from Affymetrix SNP 6.0 chips using the > oligo package. I've run into a small problem, that I think may be due to > the differences between the bioconductor package pd.genomewidesnp.6 and > the other pd.*.* annotation packages. Details are below. Any ideas? > > Thanks, > > Jeremy > > ############################################### > > # here are the names of the .CEL files > > > fullFilenamesOrigCelFiles[1:5] > [1] "rawData/tds2008/GenomeWideSNP_6/SNP001_01_M001A.CEL" > [2] "rawData/tds2008/GenomeWideSNP_6/SNP001_02_M003A.CEL" > [3] "rawData/tds2008/GenomeWideSNP_6/SNP001_03_M007A.CEL" > [4] "rawData/tds2008/GenomeWideSNP_6/SNP001_04_M015A.CEL" > [5] "rawData/tds2008/GenomeWideSNP_6/SNP001_06_M026A.CEL" > > # call justSNPRMA > > > snpRmaResults <- justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], > + verbose = TRUE, > + phenoData = NULL, > + normalizeToHapmap = TRUE) > Reading CEL files. > Normalizing to Hapmap. > Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection > In addition: Warning message: > In readChar(con, 5L, useBytes = TRUE) : > cannot open compressed file '', probable reason 'No such file or > directory' > > traceback() > 3: readChar(con, 5L, useBytes = TRUE) > 2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), > package = pkgname)) > 1: justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], verbose = TRUE, > phenoData = NULL, normalizeToHapmap = TRUE) > > sessionInfo() > R version 2.7.0 (2008-04-22) > i686-pc-linux-gnu > > locale: > C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] pd.genomewidesnp.6_0.4.1 aroma.affymetrix_0.9.1 > aroma.apd_0.1.3 > [4] R.huge_0.1.5 digest_0.3.1 > aroma.light_1.7.2 > [7] R.rsp_0.3.4 R.cache_0.1.7 > R.utils_1.0.2 > [10] R.oo_1.4.3 R.methodsS3_1.0.1 > oligo_1.4.0 > [13] oligoClasses_1.2.0 affxparser_1.11.14 > AnnotationDbi_1.2.1 > [16] preprocessCore_1.1.9 RSQLite_0.6-8 > DBI_0.2-4 > [19] Biobase_1.99.10 > > # See if we can find the problem - the following three lines come from > justSNPRMA > > > filenames <- fullFilenamesOrigCelFiles[1:5] > > headdetails <- readCelHeader(filenames[1]) > > pkgname <- cleanPlatformName(headdetails[["chiptype"]]) > > # The problematic line asks to load the following file.... > > > system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package = > pkgname) > [1] "" > > # ... which doesn't seem to exist. Here's the folder we're looking at > > > system.file("extdata", package = pkgname) > [1] "$HOME/R/i686-pc-linux-gnu- library/2.7/pd.genomewidesnp.6/extdata" > > # ... and here are the files it contains > > > list.files(system.file("extdata", package = pkgname)) > [1] "pd.genomewidesnp.6.sqlite" "seqMat.rda" > > Looks like we were trying to load a file called > "pd.genomewidesnp.6Ref.rda" from this folder. > > _______________________________________________ > 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 > The information transmitted in this electronic communica...{{dropped:10}}
ADD COMMENTlink written 11.6 years ago by Vincent J. Carey, Jr.6.3k
Answer: Problems with oligo and pd.genomewidesnp.6
0
gravatar for Vincent J. Carey, Jr.
11.6 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
i am able to reproduce this error in the devel line. very surprising because we have some unit tests for the pd.genomewide* but apparently they have not been run. i will try to get to the bottom of this. if the pd.genomewide* have to be rebuilt it may take a couple of days to push out a revision. 1: justSNPRMA(list.celfiles()) 2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package = 3: readChar(con, 5, useBytes = TRUE) Selection: 0 > sessionInfo() R version 2.8.0 Under development (unstable) (2008-05-18 r45723) 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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines stats graphics grDevices datasets utils tools [8] methods base other attached packages: [1] pd.genomewidesnp.6_0.4.1 oligo_1.5.2 oligoClasses_1.3.3 [4] affxparser_1.13.3 AnnotationDbi_1.1.35 preprocessCore_1.3.0 [7] RSQLite_0.6-8 DBI_0.2-4 Biobase_2.1.3 [10] weaver_1.5.0 codetools_0.1-3 digest_0.3.1 --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Fri, 23 May 2008, Jeremy Silver wrote: > Hello, > > I'm trying to call genotypes from Affymetrix SNP 6.0 chips using the > oligo package. I've run into a small problem, that I think may be due to > the differences between the bioconductor package pd.genomewidesnp.6 and > the other pd.*.* annotation packages. Details are below. Any ideas? > > Thanks, > > Jeremy > > ############################################### > > # here are the names of the .CEL files > > > fullFilenamesOrigCelFiles[1:5] > [1] "rawData/tds2008/GenomeWideSNP_6/SNP001_01_M001A.CEL" > [2] "rawData/tds2008/GenomeWideSNP_6/SNP001_02_M003A.CEL" > [3] "rawData/tds2008/GenomeWideSNP_6/SNP001_03_M007A.CEL" > [4] "rawData/tds2008/GenomeWideSNP_6/SNP001_04_M015A.CEL" > [5] "rawData/tds2008/GenomeWideSNP_6/SNP001_06_M026A.CEL" > > # call justSNPRMA > > > snpRmaResults <- justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], > + verbose = TRUE, > + phenoData = NULL, > + normalizeToHapmap = TRUE) > Reading CEL files. > Normalizing to Hapmap. > Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection > In addition: Warning message: > In readChar(con, 5L, useBytes = TRUE) : > cannot open compressed file '', probable reason 'No such file or > directory' > > traceback() > 3: readChar(con, 5L, useBytes = TRUE) > 2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), > package = pkgname)) > 1: justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], verbose = TRUE, > phenoData = NULL, normalizeToHapmap = TRUE) > > sessionInfo() > R version 2.7.0 (2008-04-22) > i686-pc-linux-gnu > > locale: > C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] pd.genomewidesnp.6_0.4.1 aroma.affymetrix_0.9.1 > aroma.apd_0.1.3 > [4] R.huge_0.1.5 digest_0.3.1 > aroma.light_1.7.2 > [7] R.rsp_0.3.4 R.cache_0.1.7 > R.utils_1.0.2 > [10] R.oo_1.4.3 R.methodsS3_1.0.1 > oligo_1.4.0 > [13] oligoClasses_1.2.0 affxparser_1.11.14 > AnnotationDbi_1.2.1 > [16] preprocessCore_1.1.9 RSQLite_0.6-8 > DBI_0.2-4 > [19] Biobase_1.99.10 > > # See if we can find the problem - the following three lines come from > justSNPRMA > > > filenames <- fullFilenamesOrigCelFiles[1:5] > > headdetails <- readCelHeader(filenames[1]) > > pkgname <- cleanPlatformName(headdetails[["chiptype"]]) > > # The problematic line asks to load the following file.... > > > system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package = > pkgname) > [1] "" > > # ... which doesn't seem to exist. Here's the folder we're looking at > > > system.file("extdata", package = pkgname) > [1] "$HOME/R/i686-pc-linux-gnu- library/2.7/pd.genomewidesnp.6/extdata" > > # ... and here are the files it contains > > > list.files(system.file("extdata", package = pkgname)) > [1] "pd.genomewidesnp.6.sqlite" "seqMat.rda" > > Looks like we were trying to load a file called > "pd.genomewidesnp.6Ref.rda" from this folder. > > _______________________________________________ > 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 > The information transmitted in this electronic communica...{{dropped:10}}
ADD COMMENTlink written 11.6 years ago by Vincent J. Carey, Jr.6.3k
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