Question: Help with error: 'pd.u133aaofav2 was not found in the BioConductor repository'.
0
3.0 years ago by
Juliet Hannah360
United States
Juliet Hannah360 wrote:

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:

Attempting to obtain 'pd.u133aaofav2' from BioConductor website.

Checking to see if your internet connection works...

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.

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.

pd.u133aaofav2 • 777 views
modified 2.4 years ago by sandmann.t50 • written 3.0 years ago by Juliet Hannah360

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 Since the names thus refer to a design which name has been superseded (see below), you need to explicitly state the PD package.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.

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.

0
2.4 years ago by
sandmann.t50
sandmann.t50 wrote:

As Guido pointed out, the ArrayExpress function from the ArrayExpress package does not automatically use the current Bioconductor annotation package for this array type. As this functionality is provided by the ArrayExpress package (not by gCMAPWeb), I have contacted its maintainer to highlight this problem. I also posted a workaround here: Mismatched ArrayExpress microarray annotation package. (Sorry, didn't see this question before opening a new thread.)