[BioC] Biobase geneData, geneRecommender data object

[R.T. Sweeney]

Hi, 
I am trying to use the package geneRecommender (along with Biobase) to find genes that co-vary with a query set of genes. 
I am struggling just to load my own data and the documentation is somewhat brief.
The example uses the geneData prepackaged in Biobase. I have read Biobase documentation and geneRecommender
documentation and searched extensively online for help. 

The code appears straightforward: 
> library(geneRecommender)
> data(geneData)
> my.query <- c("31613_at", "31712_at", "31497_at")
> normalized.data <- gr.normalize(geneData)
> gr.main(normalized.data, my.query, ngenes = 10

I do not understand how to get my data into a form that will load like data(geneData).
When you load the Biobase library the object geneData cannot by found with typeof or attributes. 

> typeof(geneData)
Error in typeof(geneData) : object 'geneData' not found
> class(geneData)
Error: object 'geneData' not found

However, once you run the command data(geneData) then typeof(geneData) and class(geneData) are informative.
> data(geneData)
> typeof(geneData)
[1] "double"
> class(geneData)
[1] "matrix"

Same is true with trying to write.table geneData...object not found until data(geneData) performed.
> write.table(geneData, file="geneData.txt", sep="\t", col.names = NA)
Error in inherits(x, "data.frame") : object 'geneData' not found
> data(geneData)
> write.table(geneData, file="geneData.txt", sep="\t", col.names = NA)

geneData looks like this:
                                   A           B           C            D
AFFX-MurIL2_at               192.742000   85.753300  176.757000  1.35575e+02
AFFX-MurIL10_at               97.137000  126.196000   77.921600  9.33713e+01
AFFX-MurIL4_at                45.819200    8.831350   33.063200  2.87072e+01
AFFX-MurFAS_at                22.544500    3.600930   14.688300  1.23397e+01

I have a test tab delimited file (my_data.txt) that looks like this(cDNA array data, not affy):
                S1      S2      S3      S4        S5      S6      S7     S8   
1	        NA	NA	NA	NA	-0.77	-1.02	-1.18	1.51	

With the dimensions of 186 rows and 8 columns. 

I have built an expressionSet exprs from my_data.txt, coerced into a data.frame, tried it as a matrix, and 
cannot get data(exprs) to load like data(geneData). 

> dataDirectory <- system.file("extdata", package = "Biobase")
> exprsFile <- "path/to/my_data.txt"
> exprs <- as.matrix(read.table(exprsFile, header = TRUE, sep = "\t", row.names = 1, as.is = TRUE))
> class(exprs)
[1] "matrix"
> typeof(exprs)
[1] "double"

So, exprs appears to match geneData class and typeof (shown above)

> data(exprs)
Warning message:
In data(exprs) : data set 'exprs' not found

Then, when I check exprs, I find the appropriate data which seems to match geneData attributes:
head(exprs[, 1:2])
           S1                    S2  
1        0.58                 -0.79
2        1.98                 -0.67
3         NA                   NA
4       -1.37                 -1.83
5         NA                   NA
6       1.60                   0.55
 
> attributes(exprs)
$dim
[1] 186    8

$dimnames[[1]]
    [1] "1"     "2"     "3"     "4"     "5"     "6"     "7"     "8"     "9"    
   [10] "10"    "11"    "12"    "13"    "14"    "15"    "16"    "17"    "18"   
   [19] "19"    "20"    "21"    "22"    "23"    "24"    "25"    "26"    "27"   
   [28] "28"    "29"    "30"    "31"    "32"    "33"    "34"    "35"    "36"   
etc

$dimnames[[2]]
 [1] "S1"                   
 [2] "S2"         
 [3] "S3"   
etc              

Similar to what is found looking at attributes(geneData) (but only after data(geneData) )

> attributes(geneData)
$dim
[1] 500  26
$dimnames
$dimnames[[1]]
  [1] "AFFX-MurIL2_at"              "AFFX-MurIL10_at"            
  [3] "AFFX-MurIL4_at"              "AFFX-MurFAS_at"             
  [5] "AFFX-BioB-5_at"              "AFFX-BioB-M_at"     
$dimnames[[2]]
 [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S"
[20] "T" "U" "V" "W" "X" "Y" "Z"

I am aware that this is likely a basic R issue but I have just struggled quite a few hours trying to troubleshoot
and figure this out, but can't. I need help getting my matrix input file loaded like data(geneData) in the geneRecommender example. 

Any advice would be greatly appreciated. 

Thanks, 
Robert Sweeney

> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] geneRecommender_1.24.0 Biobase_2.12.2  

loaded via a namespace (and not attached):
[1] tools_2.13.0
>