Thanks Jim,

I have found in one of the forums a response from Jason (thanks again) for
the option to set annotation.db=NULL and though force the publish command
to work with the Ids I provide in the DESeqDataSet object.

So this is now working, But I would like to have also the option to add
some annotations to the table.

Is this only possible when working directly with a data .frame?

Thanks again
Assa

On Thu, Apr 24, 2014 at 3:45 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Assa,
>
> There may well be a way to work with Ensembl IDs, and you will likely get
> an answer to your direct question from one of the maintainers.
>
> However you should note that ReportingTools simply takes the input object
> and then coerces the data to a data.frame, which is then used to create the
> HTML table. You can always create the data.frame to your own liking up
> front, and then pass that to publish(). While this is more work than just
> passing in the DESeqDataSet, you do have complete control over the output.
>
> Best,
>
> Jim
>
>
>
> On 4/24/2014 8:50 AM, Assa Yeroslaviz wrote:
>
>> Hi,
>>
>> Is it neccessary to have entrez gene IDs to work with this package?
>>
>> I am working on a dataset with Ensembl IDs. Do I need to convert them to
>> Entrez?
>>
>> When trying to create a report for a DESeqDataSet or DESeqResults objects
>> i
>> am getting the error messege:
>>
>> Error: Ids do not appear to be Entrez Ids for the specified species.
>>
>> Is there a way to work straight with the ensembl IDs?
>>
>> Thanks
>>
>> Assa
>>
>> my script:
>>
>> head(Counts_set)
>>                     A_pKO_aV_FCS G_pKO_aV_FCS M_pKO_aV_FCS D_pKO_aV
>> J_pKO_aV
>> ENSMUSG00000000001         4744         4632         4535     4748
>> 3736
>> ENSMUSG00000000003            0            0            0        0
>>  0
>> ENSMUSG00000000028         1246         1420         1429     2304
>> 1261
>> ENSMUSG00000000031            3           25           65        0
>> 50
>> ENSMUSG00000000037            0            0            0        0
>>  0
>> ENSMUSG00000000049            0            0            3        1
>>  3
>>
>> cds <- DESeqDataSetFromMatrix (
>>      countData =     Counts_set,
>>      colData   =     colData,
>>      design    = ~    condition
>>      )
>>
>> fit = DESeq(cds)
>> des2Report <- HTMLReport(shortName =paste('RNAseq_analysis_', group1, "_",
>> group2, sep=""),title ='RNA-seq analysis of differential expression using
>> DESeq2',reportDirectory = "./reports")
>> publish(fit,des2Report, pvalueCutoff=0.05,annotation.db="org.Mm.eg.db",
>> factor = colData(fit)$condition,reportDir="./reports")
>> Error: Ids do not appear to be Entrez Ids for the specified species.
>> finish(des2Report)
>>
>>
>>  sessionInfo()
>>>
>> R version 3.1.0 (2014-04-10)
>> 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] org.Mm.eg.db_2.14.0     ReportingTools_2.4.0    AnnotationDbi_1.26.0
>>   [4] Biobase_2.24.0          RSQLite_0.11.4          DBI_0.2-7
>>   [7] knitr_1.5               DESeq2_1.4.0
>>  RcppArmadillo_0.4.200.0
>> [10] Rcpp_0.11.1             GenomicRanges_1.16.2    GenomeInfoDb_1.0.2
>> [13] IRanges_1.22.3          BiocGenerics_0.10.0
>>
>> loaded via a namespace (and not attached):
>>   [1] annotate_1.42.0          AnnotationForge_1.6.0
>> BatchJobs_1.2
>>   [4] BBmisc_1.5               BiocParallel_0.6.0
>> biomaRt_2.20.0
>>   [7] Biostrings_2.32.0        biovizBase_1.12.0
>> bitops_1.0-6
>> [10] brew_1.0-6               BSgenome_1.32.0
>> Category_2.30.0
>> [13] cluster_1.14.4           codetools_0.2-8
>> colorspace_1.2-4
>> [16] dichromat_2.0-0          digest_0.6.4
>> edgeR_3.6.0
>> [19] evaluate_0.5.3           fail_1.2
>> foreach_1.4.2
>> [22] formatR_0.10             Formula_1.1-1
>> genefilter_1.46.0
>> [25] geneplotter_1.42.0       GenomicAlignments_1.0.0
>> GenomicFeatures_1.16.0
>> [28] ggbio_1.12.0             ggplot2_0.9.3.1
>> GO.db_2.14.0
>> [31] GOstats_2.30.0           graph_1.42.0
>> grid_3.1.0
>> [34] gridExtra_0.9.1          GSEABase_1.26.0
>> gtable_0.1.2
>> [37] Hmisc_3.14-4             hwriter_1.3
>> iterators_1.0.7
>> [40] lattice_0.20-24          latticeExtra_0.6-26
>> limma_3.20.1
>> [43] locfit_1.5-9.1           MASS_7.3-29
>> Matrix_1.1-2
>> [46] munsell_0.4.2            PFAM.db_2.14.0
>> plyr_1.8.1
>> [49] proto_0.3-10             RBGL_1.40.0
>> RColorBrewer_1.0-5
>> [52] RCurl_1.95-4.1           reshape2_1.2.2
>> R.methodsS3_1.6.1
>> [55] R.oo_1.18.0              Rsamtools_1.16.0
>> rtracklayer_1.24.0
>> [58] R.utils_1.29.8           scales_0.2.4
>> sendmailR_1.1-2
>> [61] splines_3.1.0            stats4_3.1.0
>> stringr_0.6.2
>> [64] survival_2.37-7          tools_3.1.0
>> VariantAnnotation_1.10.0
>> [67] XML_3.98-1.1             xtable_1.7-3
>> XVector_0.4.0
>> [70] zlibbioc_1.10.0
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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