[BioC] Creating a new instance of oligoSnpSet

[Steven McKinney]

Hello All,

I am trying to get some Illumina HumanCNV370-Quad
data into VanillaICE to do some copy number analysis.

In attempting to create an object of class "oligoSnpSet"
I can not seem to specify an annotation that works.

e.g. as specified in a vignette

> cclss <-
+   new("oligoSnpSet", copyNumber = logR, calls = gt,
+       phenoData = annotatedDataFrameFrom(logR, byrow = FALSE),
+       featureData = cclfd, annotation = "Illumina550k")
Loading required package: Illumina550k
Error in db(object) : Illumina550k package not available
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Illumina550k'
Error in dbGetQuery(db(object), sql) : 
  error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery'

or even if I specify some annotation that does exist

> cclss <-
+   new("oligoSnpSet", copyNumber = logR, calls = gt,
+       phenoData = annotatedDataFrameFrom(logR, byrow = FALSE),
+       featureData = cclfd, annotation = "hgu133plus2cdf")
Loading required package: hgu133plus2cdf
Error in db(object) : 
  trying to get slot "getdb" from an object of a basic class ("environment") with no slots
Error in dbGetQuery(db(object), sql) : 
  error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery'


Is there a way to work around this annotation bit of building
an eSet object? 

I can't figure out from documentation, reading source code, or
experimenting, as to what will work for this annotation argument.

I'm a bit hooped as there does not yet appear to be annotation
for the Illumina HumanCNV370-Quad, but I have annotation
information from other files from Illumina etc.

Can I put some dummy object as an argument for annotation
and patch it up with my known info?

Any ideas?


Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada