[BioC] affylmGUI gene list from Venn diagram, was: (no subject)

[Simon Kidd]

At 11:51am +1000 19/6/04, James Wettenhall wrote:
>On Fri, 18 Jun 2004, Simon Kidd wrote:
>>  >class(a) <- "matrix"
>>  >data.frame(geneIDs=geneIDs,a)
>
>>  This worked right upto the end where it gave me the following error message:
>>
>>  >  data.frame(geneIDs=geneIDs,a)
>>  Error in data.frame(geneIDs = geneIDs, a) :
>>	arguments imply differing number of rows: 14010, 8
>
>Sorry, my mistake.  What you need to use in the data.frame is
>the 'clas' object from classifyTestsF, not the 'a' object
>from vennCounts.
>
>clas <- classifyTestsF(tstat,df=10,p.value=0.05)
>class(clas) <- "matrix"
>data.frame(geneIDs=geneIDs,clas)

With this I get a slightly different error message, here is what I 
typed and the error message:
--------------
load("rma.lma")
tstat <- ContrastParameterizationList[[1]]$eb$t
tstat <- matrix(rt(300,df=10),100,3)
tstat[1:33,] <- tstat[1:33,]+2
clas <- classifyTestsF(tstat,df=10,p.value=0.05)
a <- vennCounts(clas)
geneIDs <- ls(getCdfInfo(RawAffyData))
class(clas) <- "matrix"
data.frame(geneIDs=geneIDs,clas)

Error in data.frame(geneIDs = geneIDs, clas) :	arguments imply 
differing number of rows: 14010, 100

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

I dont know if it matters but I have eight targets of which only four 
are used for contrasts, will that make a difference?

thanks for your help.

Simon