[BioC] how to give input to geneAnswer

Gilbert Feng g-feng at northwestern.edu
Thu Sep 30 18:22:09 CEST 2010

Hi, Budhayash

Just like steve stated, you can find the description in vignette about 
how to build a geneInput for GeneAnswers.

Basically, the essential input is a vector of genes (Current version 
only supports Entrez IDs). But if you have any values associated with 
these genes, like foldchange, p-value, etc, the input can be a matrix or 
dataframe. In this case, the 1st column is always for gene Entrez IDs. 
You can find a case by this:


       GeneID foldChange       pValue
374      374  17.553825 1.241073e-11
2289    2289  10.549139 5.513686e-14
10563  10563  10.688601 1.073456e-10
687      687   6.112663 1.351898e-09
80149  80149   4.939585 6.473841e-09
5033    5033   4.265287 1.341238e-06

row names can be null.



On 9/30/10 7:50 AM, Steve Lianoglou wrote:
> Hi,
> On Thu, Sep 30, 2010 at 4:07 AM, Budhayash Gautam
> <budhayashgautam at gmail.com>  wrote:
>> hello everyone
>> please tell me that how can we give input or
>> in what manner we can give input to geneanswer
>> thanks in advance
> Did you read through the vignette for the package?
> http://www.bioconductor.org/packages/2.6/bioc/vignettes/GeneAnswers/inst/doc/geneAnswers.pdf
> -steve

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