[BioC] help: goseq and makeOrgPackageFromNCBI in AnnotationForge

[Marc Carlson]

Hi,

So your 1st problem was caused by a small bug that I have now fixed (you 
should be able to get the fix in a day or so). But the other problem is 
much more serious. It's caused by the fact that there just isn't any GO 
information available for your organism at NCBI OR at blast2GO. So for 
that to work you are going to have to find some GO data. Alternatively, 
you could use makeOrgPackage() directly and just make an organism 
package from whatever data frames of annotation data it is that you have 
available. There is a vignette here that you can look at for more 
information:

http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html


Marc




On 11/06/2013 12:31 AM, 刘鹏飞 wrote:
>   Hi  all and M. Carlson
> I am now working on an archaea, which is not a common organism. I want to
> use goseq to do the GO analysis of my RNAseq data.In order to creat the
> category mappings(relationship between GO and gene id), I try to use the
> makeOrgPackagesFromNCBI.Now the problem comes as following:
> 1 using the command here,
>   makeOrgPackageFromNCBI(
> +            version="0.1",
> +            maintainer="Pengfei Liu <liupfskygre at gmail.com>",
> +            author="Pengfei Liu <liupfskygre at gmail.com>",
> +            outputDir=".",
> +            tax_id="1041930",
> +            genus="Methanocella",
> +            species="conradii",NCBIFilesDir=NULL)
> Error in makeOrgPackageFromNCBI(version = "0.1", maintainer = "Pengfei Liu <
> liupfskygre at gmail.com>",  :
>    'NCBIFilesDir' argument needs to be a single string or NULL
> 2, add NCBIFilesDir=NULL, same error
> makeOrgPackageFromNCBI(
> +            version="0.1",
> +            maintainer="Pengfei Liu <liupfskygre at gmail.com>",
> +            author="Pengfei Liu <liupfskygre at gmail.com>",
> +            outputDir=".",
> +            tax_id="1041930",
> +            genus="Methanocella",
> +            species="conradii", NCBIFilesDir=NULL)
> Error in makeOrgPackageFromNCBI(version = "0.1", maintainer = "Pengfei Liu <
> liupfskygre at gmail.com>",  :
>    'NCBIFilesDir' argument needs to be a single string or NULL
> 3 use following, it worked for a while
> makeOrgPackageFromNCBI(
>             version="0.1",
>             maintainer="Pengfei Liu <liupfskygre at gmail.com>",
>             author="Pengfei Liu <liupfskygre at gmail.com>",
>             outputDir=".",
>             tax_id="1041930",
>             genus="Methanocella",
>             species="conradii", NCBIFilesDir="/home/hp/liupf")
>
> however, following appeared and stoped
>
> Getting blast2GO data as a substitute for gene2go
> Error in .tryDL(url, tmp) :
>    After 3 attempts, AnnotationDbi is still not able to access the
>    following URL:
>    http://www.b2gfar.org/_media/species:data:1041930.annot.zip You might
>    want to try again later.
>
> Moreover, when using above command, the memeroy of my computer(8 Gb) is
> nearyly fully occupied, it is my first time to use this function,
> I do not know the memory requirement of this function?
>
> so how to solve this issuse and to successfully create a db for goseq, or
> is there any other way to do the same job?
>
> Thanks!
>
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] GO.db_2.10.1          RCurl_1.95-4.1        bitops_1.0-6
>   [4] AnnotationForge_1.4.0 org.Hs.eg.db_2.10.1   RSQLite_0.11.4
>   [7] DBI_0.2-7             AnnotationDbi_1.24.0  Biobase_2.22.0
> [10] BiocGenerics_0.8.0    BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.20.4 stats4_3.0.2   tcltk_3.0.2    tools_3.0.2
>
>