Entering edit mode
Dear all,
I am a new user of Bioconductor and I want to normalize and perform gene filtering of HTA 2.0 array.
I used oligo to perform RMA, my codes are:
> GSE1234cels = list.celfiles() > GSE1234raw = read.celfiles(GSE1234cels) > GSE1234.eset = rma(GSE1234raw, target='core') > GSE1234f <- nsFilter(GSE1234.eset)
And here is the error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘columns’ for signature ‘"AffyHTAPDInfo"’
Then I tried to install "affycoretools", and it reminded me to install "AnnotationHub" package. (Sorry, the error is in Chinese, so I don't show it here. But it means no package "AnnotationHub".)
But when I installed "AnnotationHub", I failed and the error was:
> biocLite("AnnotationHub")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.23.9), R 3.3.1 (2016-06-21).
Installing package(s) ‘AnnotationHub’
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘AnnotationHub’
These will not be installed
installation path not writeable, unable to update packages: foreign, lattice, Matrix, mgcv, survival
Old packages: 'affy', 'affyio', 'AnnotationDbi', 'Biobase', 'Biostrings', 'CLL', 'crossmeta',
'DynDoc', 'gcrma', 'GEOquery', 'IRanges', 'MergeMaid', 'metaArray', 'multtest', 'oligoClasses',
'preprocessCore', 'S4Vectors', 'stringi', 'tkWidgets', 'widgetTools', 'XVector', 'zlibbioc'
Update all/some/none? [a/s/n]:
I don't know what to do. Could anyone help me and give me some clues?
Thank you very much.
Thank you very much! Mr. Morgan. Your answer has been very helpful.
I installed "AnnotationHub" successfully with your code.
And may I ask you another question?
Yes, I installed development version of Bioconductor. But when I installed R again, I didn't see any difference between the two Rs on my PC. It lookes they are both development versions. They both have same packages installed. And at most times, I don't feel any inconvenience use either of them… Do you know how I can install another oridinary version of R? And what's the main difference of their functions?
Thank you!
You are actually using the 'release' version of R (3.3.1). Currently (until mid-October), the 'release' and 'devel' versions of Bioconductor both use the release version of R.
The version of Bioconductor in use is determined by the version of the BiocInstaller package you have installed. At some point, the version BiocInstaller installed with
source("https://bioconductor.org/biocLite.R")was updated using a command likeBiocInstaller::useDevel(). Normally, one would then need to update other packages to the devel version, as indicated byBiocInstaller::biocValid().You could revert to the release version with
BiocInstaller::useDevel(FALSE), then executeBiocInstaller::biocValid()and follow the advice (probably to re-install many packages).We are nearly at the next release; personally, I would continue to use devel until the next release, and then be sure to use the release version after that.
Packages in bioc 'devel' differ from those in release in two major ways. First, new features can be introduced into individual packages. There are many new features across all packages; individually these are often summarized in a package NEWS file and collectively at the time of each release. Second, new packages are introduced into the 'devel' branch, and only made available when the devel branch is made into the next release (approximately every April and October).
Thank you. Mr. Morgan.
Do you mean that I'm using 'release' version of R with 'devel' version of Bioconductor?
And after mid-October, I'd better use 'release' version of Bioconductor with code: BiocInstaller::useDevel(FALSE) and BiocInstaller::useDevel(FALSE)?
Thank you very much.
I'm sorry, but the first error still exists and I have no idea what the cause is.
Could you please give me some suggestions?
Thank you.