Please don't take conversations off-list.
On Friday, February 07, 2014 9:00:06 PM, Joseph Shaw wrote:
> Hi Jim,
> Thanks for all your assistance. I really appreciate it!
> Unfortunately, when I attempt to run
>> install.packages("org.Cjejuni_0.0.1.tar.gz", repos = NULL, type =
> I get the error warning
>> Error : package 'AnnotationDbi' 1.24.0 was found, but >= 1.25.2 is
required by 'org.Cjejuni.eg.db'
> I have since attempted to reinstall and update the AnnotationDbi
> package on my system to a compatible iteration, but the process
> results in the same error.
Hmm. Weird. I seem to have one iteration of a devel AnnotationDbi
package in my release BioC install.
You could probably just untar and ungzip that file and then manually
change the DESCRIPTION file to require AnnotationDbi >= 1.24.0 and
install.packages("org.Cjejuni.eg.db", type = "source", repos = NULL)
> On a separate but related note, is it possible to restrict the list
> gene annotations from org.Cjejuni.eg.db used in the GO analysis
> the GSEAGOHyperGParams()* function) to simply include the probes
> in the experiment (i.e. create two subsets; a gene universe and a
> collection of genes identified as differentially expressed)?
> (*The GSEAGOHyperGParams() function is used in the unuspported model
> organisms vignette, but the author simply uses the entire gene
> as the gene universe and selects the first 500 genes as
> expressed; ideally, I would like to include genes in the universe
> based on gene IDs, but this might not be the most efficient way.)
You are reading the wrong vignette. While this is technically a
'unsupported organism', since you have an org package, you can just
the regular infrastructure:
> univ <- Lkeys(org.Cjejuni.egACCNUM)
> gns <- univ[sample(1:1670, 100)] ## here I am just selecting genes
> p <- new("GOHyperGParams", geneIds = gns, universeGeneIds = univ,
ontology = "BP", annotation = "org.Cjejuni.eg.db", conditional = TRUE)
> hyp <- hyperGTest(p)
GOBPID Pvalue OddsRatio ExpCount Count Size
1 GO:0012501 0.003677779 Inf 0.1221239 2 2 programmed
2 GO:0016265 0.003677779 Inf 0.1221239 2 2
I get an infinite odds ratio here because I randomly selected the only
two apoptosis genes on the array. Yay for me!
> Relevant Vignette:
> On Fri, Feb 7, 2014 at 7:03 PM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote:
>> See attached.
>> On 2/6/2014 8:32 PM, Joseph Shaw wrote:
>>> Hi Jim,
>>>> You can check to see if it is a viable option by just giving it a
>>> I have attempted to call the makeOrgPackageFromNCBI() as described
>>> your previous mail (having provided my details for the author and
>>> maintainer arguments); however, the function call doesn't fully
>>> complete. In particular, the steps outline below are completed,
>>> appears to make it no further.
>>>> Loading required package: GO.db
>>>> Getting data for gene2pubmed.gz
>>>> Loading required package: RCurl
>>>> Loading required package: bitops
>>>> discarding data from other organisms
>>>> Populating gene2pubmed table:
>>>> table gene2pubmed filled
>>>> Getting data for gene2accession.gz
>>> I'm not sure if the function has failed or if the function is
>>> the process of completion. Could you tell me, approximately, how
>>> the function should take to complete? For reference, I'm currently
>>> running OS X with 1.8 GHz processor and 4GB memory.
>> James W. MacDonald, M.S.
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099