I am following the gcMap vignette:
http://www.bioconductor.org/packages/devel/bioc/vignettes/gCMAPWeb/inst/doc/referenceDatasets.pdf
The following data takes a long time to load so I have commented it out:
library( ArrayExpress )
library( affy )
# GEOD5258.batch <- ArrayExpress("E-GEOD-5258")
I obtain the following error:
Loading required package: pd.u133aaofav2
Attempting to obtain 'pd.u133aaofav2' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.u133aaofav2' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in oligo::read.celfiles(filenames = file.path(path, unique(files))) :
The annotation package, pd.u133aaofav2, could not be loaded.
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.hg.u133a’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.u133aaofav2’
Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, :
Unable to read cel files in/var/folders/3j/tzl04yg97_n60yhhhr29vr_4f7byc0/T//RtmpJRYSQc
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) :
ArrayExpress: Unable to read assay data
I then tried to install the library but received the message:
pd.u133aaofav2 is not available for R3.3.2.
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] tools_3.3.2
Does anyone have any suggestions on how to resolve this? Thanks.
FYI: 'U133AAofAv2' apparently refers to the HT-U133A arrays of that dataset. The names of the required Platform Design packages are automagically inferred from the cell files. Since the names thus refer to a design which name has been superseded (see below), you need to explicitly state the PD package. How to do this in the context of the gCMAPweb package I don't know.... but this post may be of help: help with SCAN.UPC and u133aaofav2.
In addition, from the Broad website:
HT_HG-U133A_EA: Affymetrix GeneChip Human Genome HT U133A Array, early access version (part number 520276). This array contains 676 probe sets not present on the HG-U133A array. Fifteen probe sets on the HG-U133A are absent. Data from these arrays are rendered compatible with the feature set by deleting expression values from the extra probe sets and setting the average difference values and confidence calls for the missing probe sets to 0 and 'A', respectively.
The library files for this array can be found at https://www.affymetrix.com/support/developer/tools/hta_tools.affx (where it is referred to as U133AAofAv2).
HG-U133A: Affymetrix GeneChip Human Genome U133A Array (part number 510681).
HT_HG-U133A: Affymetrix GeneChip Human Genome HT U133A Array (part number 550002). Six probe sets on the HG-U133A are absent from this array. Data from these arrays are rendered compatible with the feature set by setting the average difference values and confidence calls for the missing probe sets to 0 and 'A', respectively.