[BioC] Using ChromHeatMap with the org.Mm.eg library

[Marc Carlson]

Hi Michael,

I can't know very much about what you are doing from your post as you
have not given us much code to go on let alone a reproducible example. 
You might want to peek at the posting guide here:

http://www.bioconductor.org/help/mailing-list/posting-guide/

Anyhow, I can tell you one thing that might help: org packages do not
contain any information about probe IDs.  So if your software is asking
about probe IDs, it suggests that something you are using may be
expecting a chip package.  There are some descriptions about the
different types of annotation packages used in Bioconductor on our web
site here:

http://www.bioconductor.org/help/workflows/annotation-data/

Since you are using ChromHeatMap to try and plot RNA-seq data, I
speculate that (at a minimum) you have to make the identifiers for your
count data match the primary identifier for the annotation package.  In
this case, you are using an org package, so that would mean using an
entrez gene ID.  If you don't do this, you will probably have troubles
later on.

But I also looked at the source code for makeChrStrandData.  And in
doing so, I see the code that throws the error you described seems to
have almost nothing to do with the kind of annotation that is present. 
This error will be tripped if there are unlabeled rows in your
expression matrix.  So you need to make sure that your matrix has names
for each row and that they are all Entrez Gene IDs.


  Marc




On 08/19/2010 09:15 AM, Michael Muratet wrote:
> Greetings
>
> I am attempting to make a ChromHeatMap from RNA-seq data with Entrez
> IDs using org.Mm.eg for annotation. The original data was aligned to
> the UCSC knownGenes table and I can map the original identifiers to
> just about any other system using the browser tables. I tried
>
> > chrData <- makeChrStrandData(matrix(neuro.ca.7d), lib="org.Mm.eg")
> Error in makeChrStrandData(matrix(neuro.ca.7d), lib = "org.Mm.eg") :
>   Error: Data matrix must have row names corresponding to probe IDs.
>
> I suspect that I'm missing a step somewhere but I can't find it in the
> documentation. Is there a way to get the annotation from the org.Mm.eg
> data?
>
> Thanks
>
> Mike
>
> Session info:
>
> R version 2.11.0 (2010-04-22)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets 
> methods   base
>
> other attached packages:
>  [1] ChromHeatMap_1.2.0                 hgu95av2.db_2.4.1
>  [3] org.Hs.eg.db_2.4.1                 ALL_1.4.7
>  [5] org.Mm.eg.db_2.4.1                 RSQLite_0.8-4
>  [7] DBI_0.2-5                         
> BSgenome.Mmusculus.UCSC.mm9_1.3.16
>  [9] BSgenome_1.16.5                    Biostrings_2.16.7
> [11] GenomicRanges_1.0.5                IRanges_1.6.8
> [13] vsn_3.16.0                         limma_3.4.4
> [15] gplots_2.7.4                       caTools_1.10
> [17] bitops_1.0-4.1                     gdata_2.7.1
> [19] gtools_2.6.1                       DESeq_1.0.4
> [21] locfit_1.5-6                       akima_0.5-4
> [23] geneplotter_1.26.0                 lattice_0.18-5
> [25] annotate_1.26.1                    AnnotationDbi_1.10.0
> [27] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.26.1           affyio_1.16.0         genefilter_1.30.0    
> preprocessCore_1.10.0
>  [5] RColorBrewer_1.0-2    RCurl_1.3-1           rtracklayer_1.8.1    
> splines_2.11.0
>  [9] survival_2.35-8       tools_2.11.0          XML_2.8-1            
> xtable_1.5-6
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
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