[BioC] trouble with yeastann function in AnnBuilder

[Jacob Michaelson]

I think I finally found what I need to build a decent Yeast 2.0 
annotation package, but unfortunately, I keep getting errors.

The base file needed for yeastann is a two-column matrix containing 
probe ids and SGD accession numbers.  I created such a file by 
whittling down Affymetrix's Yeast 2.0 CSV annotation file into those 
two columns.

 From the AnnBuilder documentation for yeastann:

Arguments

base
base a matrix with two columns. The first column is probe ids and the 
second one are the mappings to SGD ids used by all the Yeast Genome 
data files. If base = "", the whole genome will be mapped based on a 
data file that contains mappings between all the ORFs and SGD ids

I then imported the above file into R using:

 > yeastsgd=read.csv("yeastsgd.csv")

and then

 > yeastsgd=as.matrix(yeastsgd)

...just to be safe (although I also tried without and still got errors).

Then I pasted the default function from the yeastann documentation, 
substituting my yeastsgd matrix into the base =" " position as follows:

yeastAnn(base = yeastsgd, yGenoUrl =
+                  
"ftp://genome-ftp.stanford.edu/pub/yeast/data_download/",
+                  yGenoNames =
+                  c("literature_curation/gene_literature.tab",
+                  "chromosomal_feature/SGD_features.tab",
+                  "literature_curation/gene_association.sgd"), toKeep =
+                  list(c(6, 1), c(9, 2, 5, 6, 8, 11, 3), c(2, 5, 7)),
+                  colNames = list(c("sgdid", "pmid"), c("sgdid",
+                  "genename", "chr", "chrloc", "chrori", "description",
+                  "alias"), c("sgdid", "go")), seps = c("\t", "\t",
+                  "\t"), by = "sgdid")

which immediately produced the error message (FYI in the "base" 
position I tried both with and without quotes, both of which produced 
errors):

Error in file(file, "r") : unable to open connection
In addition: Warning messages:
1: the condition has length > 1 and only the first element will be used 
in: if (probe2ORF == "") {
2: only first element of `description' argument used
3: cannot open file `1769308_at'

I'm not sure why it keeps misunderstanding a matrix when the 
documentation specifically calls for a matrix (for some reason it 
thinks 1769308_at is a file and not a probe).

I verified that the imported data contains the data in the proper 
placement, which it does, and the dimensions seem to be correct:

 > dim(yeastsgd)
[1] 10928     2

Also FYI here's the error message when the above yeastann function is 
implemented and yeastsgd is imported using read.csv, but not as.matrix:

Error in read.table(probe2ORF, sep = "\t", header = FALSE, strip.white 
= TRUE) :
	argument 'file' must be a character string or connection
In addition: Warning message:
the condition has length > 1 and only the first element will be used 
in: if (probe2ORF == "") {

I'd really appreciate any help or suggestions.

Thanks!

--Jake Michaelson

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