I am using R studio 3.3.1, and attempting to use 'make.cdf.package' from a cdf for the Clariom_D_Human.r1.Gene.cdf as obtained from Affymetrix and following this tutorial.
after calling 'make.cdf.package'
make.cdf.package("Clariom_D_Human.r1.Gene.CDF", cdf.path = "C:/Users/..../Clariom_D_Human.r1.Gene.CDF", compress = FALSE, species = "Homo_sapiens", package.path = pkgpath)
I get the following error:
"Error in isCDFXDA(file.path(path.expand(cdf.path), filename)):
Unable to open this file C:/Users/.../Clariom_D_Human.r1.Gene.CDF"
I obviously put in the whole path, simply for ease of typing have abbreviated it here. This as a result has made it so that I am unable to process the data or normalize it. I have called both AffyMetrix and the Laboratory whom preformed the MicroArray and was met with "we do not support this on third party programs" and "we couldn't get it to work either so we just used affy expression console" consecutively.
Suggestions of perhaps it is not yet supported by Bioconductor have also come in, but as I am attempting to treat it as a custom CDF this should not be of issue.
Thank you for any help
So I ran the code, and am getting a strsplit error, as this is not a table within R, but a file outside of R I am not sure of the preferred method to coerce it to character arguments.
> seed <- new("AffyHTAPDInfoPkgSeed", pgfFile = "Clariom_D_Human.r1.pgf",clfFile = "Clariom_D_Human.r1.clf", coreMps = "Clariom_D_Human.r1.mps",
transFile = "Clariom_D_Human.na36.hg38.transcript.csv", probeFile =
"Clariom_D_Human.na36.hg38.probeset.csv", author = my name",
email = "my email", version = "0.0.1") > makePdInfoPackage(seed)
============================================
Building annotation package for Affymetrix HTA Array
PGF.........: Clariom_D_Human.r1.pgf
CLF.........: Clariom_D_Human.r1.clf
Probeset....: Clariom_D_Human.na36.hg38.probeset.csv
Transcript..: Clariom_D_Human.na36.hg38.transcript.csv
Core MPS....: Clariom_D_Human.r1.mps
============================================
Parsing file: Clariom_D_Human.r1.pgf... OK
Parsing file: Clariom_D_Human.r1.clf... OK
Creating initial table for probes... OK
Creating dictionaries... OK
Parsing file: Clariom_D_Human.na36.hg38.probeset.csv... OK
Parsing file: Clariom_D_Human.r1.mps... Error in
strsplit(mps[["probeset_list"]], " ") : non-character argument
edited: formatting code.
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Anyway, here's what I get:
> dir() [1] "Clariom_D_Human.affymetrix.report_thresholds" [2] "Clariom_D_Human_Analysis.r1.zip" [3] "Clariom_D_Human.exon_analysis_configuration" [4] "Clariom_D_Human.na36.hg38.probeset.csv" [5] "Clariom_D_Human.na36.hg38.probeset.csv.zip" [6] "Clariom_D_Human.na36.hg38.transcript.csv" [7] "Clariom_D_Human.na36.hg38.transcript.csv.zip" [8] "Clariom_D_Human.r1.bgp" [9] "Clariom_D_Human.r1.clf" [10] "Clariom_D_Human.r1.mps" [11] "Clariom_D_Human.r1.pgf" [12] "Clariom_D_Human.r1.ps" [13] "Clariom_D_Human.r1.qcc" [14] "XTAArray_NetAffx-CSV-Files.README.txt" > seed <- new("AffyHTAPDInfoPkgSeed", clfFile = dir()[9], pgfFile = dir()[11], coreMps = dir()[10], transFile = "Clariom_D_Human.na36.hg38.transcript.csv", probeFile = "Clariom_D_Human.na36.hg38.probeset.csv", author = "me", email = "me@mine.org", version = "0.0.1") > makePdInfoPackage(seed) ================================================================================ Building annotation package for Affymetrix HTA Array PGF.........: Clariom_D_Human.r1.pgf CLF.........: Clariom_D_Human.r1.clf Probeset....: Clariom_D_Human.na36.hg38.probeset.csv Transcript..: Clariom_D_Human.na36.hg38.transcript.csv Core MPS....: Clariom_D_Human.r1.mps ================================================================================ Parsing file: Clariom_D_Human.r1.pgf... OK Parsing file: Clariom_D_Human.r1.clf... OK Creating initial table for probes... OK Creating dictionaries... OK Parsing file: Clariom_D_Human.na36.hg38.probeset.csv... OK Parsing file: Clariom_D_Human.r1.mps... OK Creating package in ./pd.clariom.d.human Inserting 950 rows into table chrom_dict... OK Inserting 5 rows into table level_dict... OK Inserting 3 rows into table type_dict... OK Inserting 138745 rows into table core_mps... OK Inserting 1562457 rows into table featureSet... OK Inserting 8132393 rows into table pmfeature... OK Inserting 711 rows into table mmfeature... OK Counting rows in chrom_dict Counting rows in core_mps Counting rows in featureSet Counting rows in level_dict Counting rows in mmfeature Counting rows in pmfeature Counting rows in type_dict Creating index idx_pmfsetid on pmfeature... OK Creating index idx_pmfid on pmfeature... OK Creating index idx_fsfsetid on featureSet... OK Creating index idx_core_meta_fsetid on core_mps... OK Creating index idx_core_fsetid on core_mps... OK Creating index idx_mmfsetid on mmfeature... OK Creating index idx_mmfid on mmfeature... OK Saving DataFrame object for PM. Saving DataFrame object for MM. Saving NetAffx Annotation... OK Done. > install.packages("pd.clariom.d.human/", repos = NULL) * installing *source* package ‘pd.clariom.d.human’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (pd.clariom.d.human) > sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pd.hta.2.0_3.12.1 pd.clariom.d.human_0.0.1 pdInfoBuilder_1.37.1 [4] oligo_1.37.2 Biostrings_2.40.2 XVector_0.12.0 [7] IRanges_2.6.1 S4Vectors_0.10.2 oligoClasses_1.35.0 [10] affxparser_1.44.0 RSQLite_1.0.0 DBI_0.4-1 [13] Biobase_2.32.0 BiocGenerics_0.18.0 loaded via a namespace (and not attached): [1] GenomicRanges_1.24.2 splines_3.3.0 [3] zlibbioc_1.18.0 bit_1.1-12 [5] foreach_1.4.3 GenomeInfoDb_1.8.3 [7] tools_3.3.0 SummarizedExperiment_1.2.3 [9] ff_2.2-13 iterators_1.0.8 [11] preprocessCore_1.34.0 affyio_1.42.0 [13] codetools_0.2-14 BiocInstaller_1.22.3If you are using an outdated version of R/BioC, then you need to upgrade.
I did upgrade and that seemed to make it work, up until install of the created package, at which point I got an error stating the package was not compatable with R. 3.3.1 (so I tried it all again in R 3.3.0 and got the same error)
Did you build the package using the same R/Bioc installation that you tried to install on? As I showed, this builds and installs on R-3.3.0/Bioc-3.3 without problems. You are being mysterious and neglecting to show the code and output you got, as well as sessionInfo(), so I have to resort to guesses.
My apologies, when I have done it with R 3.3.1 that is where I install it. Just as with R 3.3.0 I generate it and attempt to install it there. I have posted the full code and than bellow that my general question. I have included a traceback and the session info.
Creating index idx_pmfsetid on pmfeature... OKCreating index idx_pmfid on pmfeature... OK
Creating index idx_fsfsetid on featureSet... OK
Creating index idx_core_meta_fsetid on core_mps... OK
Creating index idx_core_fsetid on core_mps... OK
Creating index idx_mmfsetid on mmfeature... OK
Creating index idx_mmfid on mmfeature... OK
Saving DataFrame object for PM.
Saving DataFrame object for MM.
Saving NetAffx Annotation... OK
Done.
> install.packages("pd.clariom.d.human/", repos = NULL)
Installing package into ‘C:/Users/David C Aughton/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
Error in install.packages : type == "both" cannot be used with 'repos = NULL'
> traceback()
4: stop("directory '", pkgdir, "' exists; use unlink=TRUE ", "to remove it, or choose another destination directory")
3: createPackage(pkgname = pkgName, destinationDir = destDir, originDir = templateDir,
symbolValues = syms, quiet = quiet)
2: makePdInfoPackage(seed)
1: makePdInfoPackage(seed)
Warning messages:
1: In .HTMLsearch(query) : Unrecognized search field: title
2: In .HTMLsearch(query) : Unrecognized search field: keyword
3: In .HTMLsearch(query) : Unrecognized search field: alias
4: In .HTMLsearch(query) : Unrecognized search field: title
5: In .HTMLsearch(query) : Unrecognized search field: keyword
6: In .HTMLsearch(query) : Unrecognized search field: alias
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:[1] stats4 parallel stats graphics
[5] grDevices utils datasets methods
[9] base
other attached packages:[1] pdInfoBuilder_1.37.1
[2] oligo_1.37.2
[3] Biostrings_2.41.4
[4] XVector_0.13.7
[5] IRanges_2.7.14
[6] S4Vectors_0.11.13
[7] oligoClasses_1.35.0
[8] affxparser_1.45.0
[9] RSQLite_1.0.0
[10] DBI_0.5
[11] Biobase_2.33.3
[12] BiocGenerics_0.19.2
[13] BiocInstaller_1.23.9
[14] affyio_1.43.0
loaded via a namespace (and not attached):[1] splines_3.3.0
[2] GenomicRanges_1.25.93
[3] zlibbioc_1.19.0
[4] bit_1.1-12
[5] lattice_0.20-33
[6] foreach_1.4.3
[7] GenomeInfoDb_1.9.8
[8] tools_3.3.0
[9] SummarizedExperiment_1.3.82
[10] grid_3.3.0
[11] ff_2.2-13
[12] iterators_1.0.8
[13] preprocessCore_1.35.0
[14] Matrix_1.2-7.1
[15] codetools_0.2-14
From reading the install.packages() help pages I know the repos = NULL specifies that it can be something besides just a URL. Yet this is also the line of code that the error is calling on. Had to remove some of the package formation portion in code due to character limits.
Here's the part of interest.
> install.packages("pd.clariom.d.human/", repos = NULL) Installing package into ‘C:/Users/David C Aughton/Documents/R/win-library/3.3’ (as ‘lib’ is unspecified) Error in install.packages : type == "both" cannot be used with 'repos = NULL'And you could have read that and said 'what is this type argument you speak of, R?'. And then looked at the help page for install.packages, which says
Usage: install.packages(pkgs, lib, repos = getOption("repos"), contriburl = contrib.url(repos, type), method, available = NULL, destdir = NULL, dependencies = NA, type = getOption("pkgType"), configure.args = getOption("configure.args"), configure.vars = getOption("configure.vars"), clean = FALSE, Ncpus = getOption("Ncpus", 1L), verbose = getOption("verbose"), libs_only = FALSE, INSTALL_opts, quiet = FALSE, keep_outputs = FALSE, ...)Which is suitably mysterious. I mean, what is this getOption("pkgType") business?
> getOption("pkgType")
[1] "both"
So by default the type argument is 'both'. And if you then read the blahblahblah under Binary packages in the help file, it will bore you with all this stuff about Windows and MacOS having binary and source packages and whatnot. The upshot being that you can hypothetically install either a source package (which is what you have) or a binary package (which is not what you have), and if you say repos = NULL, you can't say you have 'both' because obviously you don't. Instead, you have to say what type of package you do have, which means that you need to include a type = "source" to over-ride the default.