[BioC] subset in XPS

[cstrato]

Dear Zhibin

In general, xps offers two ways to get the treenames from an ExprTreeSet:

1. method treeNames applied to the ExprTreeSet:
 > treenames <- treeNames(data.rma)
 > treenames

2. function getTreeNames applied to the root file directly:
 > treenames <- getTreeNames("Test3RMA.root")
 > treenames
 > treenames <- getTreeNames("Test3RMA.root","mdp")
 > treenames

Then you can select the treenames of interest by doing:
 > treenames <- treenames[c(2,4)]

Of course, the following also works:
 > value <- exprs(data.rma)
 > treenames <- colnames(value)
 > treenames
 > treenames <- treenames[c(4,6)]

In any case you get the subset:
 > sub.rma <- data.rma
 > exprs(subset.rma, treenames) <- value
 > str(sub.rma)

which results in:
  ..@ treenames:List of 2
  .. ..$ : chr "TestA2.mdp"
  .. ..$ : chr "TestB2.mdp"

Could you please send me the code you used for subsetting, which 
resulted in an "X" in front of treenames.

Do above mentioned solutions result in the same error?

Furthermore, could you give me the following information:
- which version of ROOT did you install?
- did you install the ROOT binary or compile from source?
- did you download/install the xps binary or compile from source?

P.S.:
I am glad to hear that running R through Terminal on your Mac works fine.

Best regards
Christian


Zhibin Lu wrote:
> Dear Christian,
>
> When I tried to use str(sub.rma) to check the sub set, I found there was an extra 'X' in front of each tree name. For the example you provided, the treenames were:
> .. at treenames:List of 2
> .. ..$ : chr "XTestA2.mdp"
> .. ..$ : chr "XTestB1.mdp"
>
> When I applied filters to the sub.rma, I got an error "ERROR: Could not get tree .". After I changed the treenames manually, the error was gone.
>
> I was running R 2.8/BioC 2.3 and xps 1.1.2 under Ubuntu 8.04.
>
> Regards,
>
> Zhibin
>
>