[BioC] Error message when working with sam

[James W. MacDonald]

Hi Assa,

Assa Yeroslaviz wrote:
> Hi,
> 
> I'm trying to link my sig. genes with the web. by doing so I tried both
> sam2html and link.siggenes:
> 
> sam2html(samresult, 20, "samresults_overview.html", chipname="ath1121501")
> 
> link.siggenes(samresult, 20, filename="samresults.html", addDataFrame =
> TRUE, title="SAM results - stress",
>         entrez = FALSE, refseq = FALSE, symbol = TRUE, omim = FALSE, ug =
> FALSE,
>         fullname = TRUE, which.refseq = "NM", chipname="ath1121501",
> cdfname="ath1121501")
> 
> I keep getting the error messagees:
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>   variable "ath1121501ENTREZID" was not found

That's because there are no mappings between this chip and Entrez Gene 
IDs in the ath11215001.db package. You can see what mappings do exist by 
loading the package and then using the ls() function:

 > library(ath1121501.db)
Loading required package: AnnotationDbi
Loading required package: DBI
 > ls(2)
  [1] "ath1121501"             "ath1121501_dbconn" 
"ath1121501_dbfile"
  [4] "ath1121501_dbInfo"      "ath1121501_dbschema" 
"ath1121501ACCNUM"
  [7] "ath1121501ARACYC"       "ath1121501ARACYCENZYME" "ath1121501CHR" 

[10] "ath1121501CHRLENGTHS"   "ath1121501CHRLOC" 
"ath1121501CHRLOCEND"
[13] "ath1121501ENZYME"       "ath1121501ENZYME2PROBE" 
"ath1121501GENENAME"
[16] "ath1121501GO"           "ath1121501GO2ALLPROBES" 
"ath1121501GO2PROBE"
[19] "ath1121501MAPCOUNTS"    "ath1121501ORGANISM"     "ath1121501PATH" 

[22] "ath1121501PATH2PROBE"   "ath1121501PMID" 
"ath1121501PMID2PROBE"
[25] "ath1121501SYMBOL"


If you look at the help for the functions you are trying to use, you 
will see that there is an 'entrez' argument that you can set to FALSE so 
it won't try to do Entrez Gene mappings. Depending on what mappings do 
exist in this annotation package, you may need to set other arguments to 
FALSE as well.

Best,

Jim


> 
> Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
> ifnotfound = NA) :
>   error in evaluating the argument 'envir' in selecting a method for
> function 'mget'
> 
> so I was forced toturn them off. Is there a way of using this information.
> I'm using R2.8.1 with Bioconductior 2.3. (I think)
> 
> THX,
> 
> Assa
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826