It worked.
I have now a very nice and useful report; I ma so happy.
Thank yo very very much,
Ugo 


From: Michael Lawrence <lawrence.michael@gene.com>
Date: Mon, 10 Feb 2014 09:12:16 -0800
To: "James W. MacDonald" <jmacdon@uw.edu>
Cc: Ugo Borello <ugo.borello@inserm.fr>, "bioconductor@r-project.org"
<bioconductor@r-project.org>
Subject: Re: [BioC] ReportingTools and gene annotation




On Mon, Feb 10, 2014 at 7:28 AM, James W. MacDonald <jmacdon@uw.edu> wrote:
> Hi Ugo,
> 
> 
> On 2/10/2014 6:02 AM, Ugo Borello wrote:
>> Good morning,
>> I am using ReportingTools with DESeq2 and I am not able to add the gene
>> annotation to my final report.
>> I have ensembl gene id as identifiers and not entrez id!
>> 
>> I followed Jason's suggestions as described here:
>> 
>> http://article.gmane.org/gmane.science.biology.informatics.conductor/51995/m
>> <http://article.gmane.org/gmane.science.biology.informatics.conductor/51995/m
>> > 
>> atch=
>> 
>> But the add.anns() functions doesn't work in my hands.
>> 
>>> mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl")
>>> add.anns <- function(df, mart, ...)
>> + {
>> +   nm <- rownames(df)
>> +   anns <- getBM(
>> +     attributes = c("ensembl_gene_id", "external_gene_id", "description"),
>> +     filters = "ensembl_gene_id", values = nm, mart = mart)
>> +   anns <- anns[match(nm, anns[, 1]), ]
>> +   colnames(anns) <- c("ID", "Gene Symbol", "Gene Description")
>> +   df <- cbind(anns, df[, 2:nrow(df)])
> 
> Note that in the line above you are subsetting 'df' by column, using the
> number of rows. I am not sure if you want to eliminate the first column here
> (as you are using the rownames to annotate, so I don't know what the first
> column contains). But it is simpler to eliminate the first column than to keep
> the 2:ncol(columns):
> 
> df <- cbind(anns, df[,-1])
> 

To be safe you'll want 

df <- cbind(anns, df[,-1,drop=FALSE])

> Best,
> 
> Jim
> 
>> +   rownames(df) <- nm
>> +   df
>> + }
>>> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF =
>> list(add.anns, modifyReportDF), mart = mart)    ## dds is the DESeqDataSet
>> object
>> 
>>   Show Traceback
>>   Rerun with Debug
>>   Error in `[.data.frame`(df, , 2:nrow(df)) : undefined columns selected
>> 
>> I also tried this:
>>> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF =
>> list(add.anns, modifyReportDF), mart = mart, df= counts(dds))  # dds is the
>> DESeqDataSet object
>> 
>>   Show Traceback
>>   Rerun with Debug
>>   Error in df[, 2:nrow(df)] : subscript out of bounds
>> 
>> 
>> What am I doing wrong?
>> 
>> Is there a simple way of adding my annotation to the HTML report?
>> 
>>   ENSEMBL                          ENTREZID SYMBOL     GENENAME
>> 1 ENSMUSG00000000001    14679   Gnai     guanine nucleotide binding protein
>> (G protein), alpha inhibiting 3
>> 2 ENSMUSG00000000028    12544  Cdc45   cell division cycle 45
>> 3 ENSMUSG00000000031       NA     NA      NA
>> 4 ENSMUSG00000000037   107815  Scml2  sex comb on midleg-like 2 (Drosophila)
>> 5 ENSMUSG00000000049    11818   Apoh    apolipoprotein H
>> 6 ENSMUSG00000000056    67608   Narf     nuclear prelamin A recognition
>> factor
>> 
>> 
>> Thank you
>> 
>> Ugo
>> 
>> 
>>> sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> base
>> 
>> other attached packages:
>>   [1] ReportingTools_2.2.0    knitr_1.5               org.Mm.eg.db_2.10.1
>> RSQLite_0.11.4          DBI_0.2-7
>>   [6] AnnotationDbi_1.24.0    Biobase_2.22.0          DESeq2_1.2.9
>> RcppArmadillo_0.4.000.2 Rcpp_0.10.6
>> [11] GenomicRanges_1.14.4    XVector_0.2.0           IRanges_1.20.6
>> BiocGenerics_0.8.0      biomaRt_2.18.0
>> 
>> loaded via a namespace (and not attached):
>>   [1] annotate_1.40.0          AnnotationForge_1.4.4    Biostrings_2.30.1
>> biovizBase_1.10.7        bitops_1.0-6
>>   [6] BSgenome_1.30.0          Category_2.28.0          cluster_1.14.4
>> colorspace_1.2-4         dichromat_2.0-0
>> [11] digest_0.6.4             edgeR_3.4.2              evaluate_0.5.1
>> formatR_0.10             Formula_1.1-1
>> [16] genefilter_1.44.0        GenomicFeatures_1.14.2   ggbio_1.10.10
>> ggplot2_0.9.3.1          GO.db_2.10.1
>> [21] GOstats_2.28.0           graph_1.40.1             grid_3.0.2
>> gridExtra_0.9.1          GSEABase_1.24.0
>> [26] gtable_0.1.2             Hmisc_3.14-0             hwriter_1.3
>> labeling_0.2             lattice_0.20-24
>> [31] latticeExtra_0.6-26      limma_3.18.10            locfit_1.5-9.1
>> MASS_7.3-29              Matrix_1.1-2
>> [36] munsell_0.4.2            PFAM.db_2.10.1           plyr_1.8
>> proto_0.3-10             R.methodsS3_1.6.1
>> [41] R.oo_1.17.0              R.utils_1.28.4           RBGL_1.38.0
>> RColorBrewer_1.0-5       RCurl_1.95-4.1
>> [46] reshape2_1.2.2           Rsamtools_1.14.2         rtracklayer_1.22.3
>> scales_0.2.3             splines_3.0.2
>> [51] stats4_3.0.2             stringr_0.6.2            survival_2.37-7
>> tools_3.0.2              VariantAnnotation_1.8.10
>> [56] XML_3.95-0.2             xtable_1.7-1             zlibbioc_1.8.0
>> 
>> _______________________________________________
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>> <http://news.gmane.org/gmane.science.biology.informatics.conductor>
> 
> -- 
> 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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