[BioC] Help with getBM using EST ids from zebrafish
Ochsner, Scott A
sochsner at bcm.tmc.edu
Thu Dec 4 21:14:13 CET 2008
I am trying to retrieve zfin annotation for each of my 6000+ zebrafish EST ids using biomaRt. As an example of the EST ids I've included the output from NCBI's EST search for CO349769.
1. DR_AOV_FL01_G08 adult ovary full-length (TLL) Danio rerio cDNA, mRNA sequence
As a further note, searching UniGene is successful with "CO349769", but not with "49431086". I've set up the following:
Question1: If ESTs are mapped (based on previous posts they don't look like they are), what is the appropriate filter variable in the line of code below?
Question2: If it turns out ESTs are not mapped, I'll probably have to go through UniGene to obtain an ID I can use with biomaRt. Does anyone know of a way to batch search UniGene? 6000+ ids is a lot to search one by one.
Thanks for any help,
R version 2.8.0 (2008-10-20)
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
 splines tools stats graphics grDevices utils datasets methods base
other attached packages:
 biomaRt_1.16.0 genefilter_1.22.0 survival_2.34-1 geneplotter_1.20.0 annotate_1.20.0 xtable_1.5-4 AnnotationDbi_1.4.0 lattice_0.17-15
 limma_2.16.2 affy_1.20.0 Biobase_2.2.0
loaded via a namespace (and not attached):
 affyio_1.10.0 DBI_0.2-4 grid_2.8.0 KernSmooth_2.22-22 preprocessCore_1.4.0 RColorBrewer_1.0-2 RCurl_0.91-0
 RSQLite_0.7-1 XML_1.94-0.1
Scott A. Ochsner, Ph.D.
Molecular and Cellular Biology
Baylor College of Medicine
Houston, TX. 77030
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