[BioC] problem about hgu133plus2 annotation

Marc Carlson mcarlson at fhcrc.org
Thu Jul 22 18:38:19 CEST 2010


Hi Gina,

I am afraid it's a little hard to tell what is going on here.  For
example, I don't see sessionInfo() so it is hard to tell what you were
running.  And I only have enough code to wildly speculate about what you
were doing.  You might want to see our posting guide here:

http://www.bioconductor.org/docs/postingGuide.html



  Marc



On 07/22/2010 02:11 AM, Gina Liao wrote:
> Dear All,
> I have 20 chips, and I used R to standardize the CEL files.Then, i got an expression value data of all chips.And I also downloaded the annotation csv format from NetAffy.(HG-U133_Plus_2 Annotations, CSV format, Release 30 (22 MB, 11/15/09))
> Here's my code. 
> ########test = justRMA()eset.st = standardise(test)
> exprs.st = exprs(eset.st)e.out = exprs.stdim(e.out) #* 54675 20########
> However, i found out that the order of the rownames(e.out) is a little different to the row name of hgu133plus2.csv. The order from 54630 to 54640 is not the same to these two rows. 
> They should be the same,right? Is "hgu133plus2cdf" the problem? How could I solve it?
> Thanks!!!!! 
> Best,Gina 		 	   		  
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