[BioC] oneChannelGUI and hugene10stv1cdf

[Steve Taylor]

Hi,

I am trying to run oneChannelGUI, analysing data based on the Affy Gene 1.0 ST Array.

I installed the library from http://www.bioinformatica.unito.it/downloads/hugene10stv1cdf_1.0.0.tar.gz (I am not sure how legitimate this is :-) ).

When running the 'Table of genes ranked in order of differential expression' option in oneChannelGUI it generated several errors (in the tcl/tk interface,see below) and wouldn't generate the top table 
of results. It looks like it is trying to load 'hugene10stv1' rather than 'hugene10stv1cdf'. If this is the problem, is there a workaround or an official hugene10stv1 library that works with this package?

Errors in R Shell
=================
 > ls()
[1] "affylmGUIenvironment" "ReturnVal"
Warning messages:
1: In file(con, "r") :
   file("") only supports open = "w+" and open = "w+b": using the former
2: In file(con, "w") :
   file("") only supports open = "w+" and open = "w+b": using the former
3: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) :
   Estimation of var.prior failed - set to default value
4: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) :
   Estimation of var.prior failed - set to default value
5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
   there is no package called 'hugene10stv1'
 > library("hugene10stv1")
Error in library("hugene10stv1") :
   there is no package called 'hugene10stv1'

Errors in Tcl/Tk OneChannelGUI
==============================
Error in stop("need data package: ", annlib) : object "annlib" not found

Error in get(paste(lib, name, sep = ""), mode = "environment"): variable "hugene10stv1ENTREZID" of mode "environment" was not found

Error in get(paste(lib, name, sep = ""), mode = "environment"): variable "hugene10stv1SYMBOL" of mode "environment" was not found

Error in dim(data) <- dim : attempt to set an attribute on NULL

Error in names(x)<-value : 'names' attribute[3] must be same length as the vector[1]


==========================

 > sessionInfo()
R version 2.6.1 (2007-11-26)
sparc-sun-solaris2.9

locale:
/en_GB/C/en_GB/en_GB/en_GB/en_GB

attached base packages:
[1] tcltk     tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] hugene10stv1cdf_1.0.0 oneChannelGUI_1.4.2   tkWidgets_1.16.0
  [4] DynDoc_1.16.0         widgetTools_1.14.0    affylmGUI_1.12.0
  [7] affy_1.16.0           preprocessCore_1.0.0  affyio_1.6.1
[10] limma_2.12.0          Biobase_1.16.2

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

Thanks for any help,

Steve
==========================================
Medical Sciences Division
Weatherall Institute of Molecular Medicine
Oxford University