[BioC] trouble with yeastann function in AnnBuilder

[James W. MacDonald]

Jacob Michaelson wrote:
> 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

Although it states here that base is supposed to be a matrix with two 
columns, really what it is supposed to be is a _file_ containing a 
matrix with two columns. The file should be in your working directory.
> 
> 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 == "") {

So this error is basically saying that R looked for the file 'yeastsgd' 
in the current working directory, and couldn't find it.


HTH,

Jim


> 
> I'd really appreciate any help or suggestions.
> 
> Thanks!
> 
> --Jake Michaelson
> 
> 	[[alternative text/enriched version deleted]]
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109