Nianhua:

Thanks so much for your help! I am a newbie for R and I don't know how to
use SVN now, but I will learn it, could you please email me a copy of new
version of AnnBuilder package? I want to give a  try as soon as possible!
Also, I found I cannot use some of function in AnnBuilder, I don't know why?
I used it because I want to reproduce the result from AnnBuilder.pdf from
the package review. it always give me error.

Best

Shiliang




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[Previously saved workspace restored]

> library(AnnBUilder)
Error in library(AnnBUilder) : there is no package called 'AnnBUilder'
> library(AnnBuilder)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: XML
Loading required package: annotate

Attaching package: 'annotate'


        The following object(s) are masked _by_ .GlobalEnv :

         getGO

Loading required package: RSQLite
Loading required package: DBI
> writeAnnData2Pkg
Error: object "writeAnnData2Pkg" not found
> getChroLocation
Error: object "getChroLocation" not found
>



On 7/27/06, Nianhua Li <nli@fhcrc.org> wrote:
>
> Hi, Shiliang,
>
> You were right that AnnBuilder did have a bug. Thanks for the report!
>
> The bug is related to Weijun's question:
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/9227/focus=9232
> When baseType is "ll", the baseFile can't be parsed correctly because
> some parsers assume Entrez Gene is at the 3rd column of the base file.
> Thanks for John's patch, AnnBuilder just quietly converts the base file
> into three columns when baseType is "ll". So, weijun's problem got
> solved. Unfortunately, the parser used for "go2probe" mapping assumes a
> two-column setting for baseType "ll", therefore can't work correctly
> with the patch.
>
> Now the problem has been solved. You can either get the up-to-date
> AnnBuilder (v 1.11.6) from svn or wait still Saturday noon to download
> it using biocLite or from website. You can also modify your local source
> AnnBuilder/R/ABPkgBuilder.R if you are in a hurry:
> ===================================================================
> --- ABPkgBuilder.R      (v1.11.5 or before)
> +++ ABPkgBuilder.R      (v1.11.6)
>
> # Map GO ids to probe ids that are directly associated with the GO ids
> mapGO2Probe <- function(eg, baseMapType){
> -     if(baseMapType == "ll"){
> -            parser(eg) <- file.path(.path.package("AnnBuilder"),
> -                                    "scripts", "GO2ProbeParser4LL")
> -        }else{
> -            parser(eg) <- file.path(.path.package("AnnBuilder"),
> +        parser(eg) <- file.path(.path.package("AnnBuilder"),
>                                     "scripts", "GO2ProbeParser")
> -        }
>         options(show.error.messages = FALSE)
>         go2Probe <- try(parseData(eg, eg@go, ncol = 3))
>         options(show.error.messages = TRUE)
> ====================================================================
>
> Also the probe number mismatch is because your base file has duplicated
> probeset identifiers.
>
> help it works this time :)
>
> nianhua
>
>

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