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.