[BioC] Bioconductor Digest, Vol 90, Issue 1

[Amos Folarin]

Dear YSong,

Try something like this:

# you need to specify the probesets that you want accession numbers for
in the first argument to mget
library(mouse4302.db)
mapping.pid.acc <-unlist(mget(c("1415673_at","1415675_at"),
mouse4302ACCNUM))

#>mapping.pid.acc
#1415673_at  1415675_at 
#"NM_133900"  "BC008256"


#i.e this will return all the probeid accession numbers
mapping.pid.acc <-unlist(mget(featureNames(rma.data), mouse4302ACCNUM))


Regards,
Amos Folarin


------------------------------

Message: 4
Date: Mon, 2 Aug 2010 09:18:57 +0800
From: Yisong Zhen <zhenyisong at gmail.com>
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] probe ID<-> accession number
Message-ID:
	<AANLkTi=f6RdNzqQVu0vnHTsUBq_n6vCw1hbQ1+K92UYr at mail.gmail.com>
Content-Type: text/plain

Dear All,

I  use the following code to generate HTML report on deferential
expression
genes after LIMMA analysis. The code is from Bioinformatics
and Computational Biology Solutions Using R and Bioconductor. Now, I
want to
add a column in the final output, which includes  the gene accession
number
of reference sequence, for example, NM_008725 besides gene entrez ID and
gene name. In this way,  I could match probe ID to their corresponding
accession number.

But how can I write a code to implement it?

Thanks in advance.

YiSong


PS.

library("annotate");
library("mouse4302.db");

totalGeneNumber<-dim(exprs(rma.data))[1];
iso_control<-topTable(fit2,coef=1,adjust.method="BH",number=totalGeneNum
ber);
genenames = as.character(iso_control$ID);
sym<-getSYMBOL(genenames,"mouse4302");
ll<-getEG(genenames,"mouse4302");
iso_control=data.frame(sym,signif(iso_control[,-1],3));
htmlpage(list(ll),othernames=iso_control,filename="iso_control.html",tit
le="HTML
report", table.center=TRUE, table.head=c("ENTREZ ID",
colnames(iso_control)));

	[[alternative HTML version deleted]]



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