[BioC] subset in XPS

Zhibin Lu zhbluweb at hotmail.com
Fri Jul 4 16:11:05 CEST 2008


Dear Christian,

I tested the new package with my linux box, so I compiled ROOT from source with the file 'root_v5.18.00.source.tar.gz'. Since I was using Linux, I think xps was also compiled from source. I followed your direction, it seems that the function 'exprs' gave the extra X. Here is what I got:

> treenames<-treeNames(Data.rma)
> treenames
[[1]]
[1] "10017_12.mdp"

[[2]]
[1] "100M_11.mdp"

[[3]]
[1] "11017_4.mdp"

[[4]]
[1] "110M_3.mdp"

[[5]]
[1] "11117_6.mdp"

[[6]]
[1] "111M_5.mdp"

[[7]]
[1] "9617_2.mdp"

[[8]]
[1] "96M_1.mdp"

[[9]]
[1] "9717_8.mdp"

[[10]]
[1] "97M_7.mdp"

[[11]]
[1] "9817_10.mdp"

[[12]]
[1] "98M_9.mdp"

> treenames=getTreeNames("rma_all.root")
> treenames
 [1] "10017_12.rbg" "10017_12.int" "100M_11.rbg"  "100M_11.int"  "11017_4.rbg" 
 [6] "11017_4.int"  "110M_3.rbg"   "110M_3.int"   "11117_6.rbg"  "11117_6.int" 
[11] "111M_5.rbg"   "111M_5.int"   "9617_2.rbg"   "9617_2.int"   "96M_1.rbg"   
[16] "96M_1.int"    "9717_8.rbg"   "9717_8.int"   "97M_7.rbg"    "97M_7.int"   
[21] "9817_10.rbg"  "9817_10.int"  "98M_9.rbg"    "98M_9.int"    "10017_12.cqu"
[26] "100M_11.cqu"  "11017_4.cqu"  "110M_3.cqu"   "11117_6.cqu"  "111M_5.cqu"  
[31] "9617_2.cqu"   "96M_1.cqu"    "9717_8.cqu"   "97M_7.cqu"    "9817_10.cqu" 
[36] "98M_9.cqu"    "10017_12.mdp" "100M_11.mdp"  "11017_4.mdp"  "110M_3.mdp"  
[41] "11117_6.mdp"  "111M_5.mdp"   "9617_2.mdp"   "96M_1.mdp"    "9717_8.mdp"  
[46] "97M_7.mdp"    "9817_10.mdp"  "98M_9.mdp"   

> treenames=getTreeNames("rma_all.root", "mdp")
> treenames
 [1] "10017_12.mdp" "100M_11.mdp"  "11017_4.mdp"  "110M_3.mdp"   "11117_6.mdp" 
 [6] "111M_5.mdp"   "9617_2.mdp"   "96M_1.mdp"    "9717_8.mdp"   "97M_7.mdp"   
[11] "9817_10.mdp"  "98M_9.mdp"

> value<-exprs(Data.rma)
> treenames<-colnames(value)
> treenames
 [1] "UNIT_ID"             "UnitName"            "X10017_12.mdp_LEVEL"
 [4] "X100M_11.mdp_LEVEL"  "X11017_4.mdp_LEVEL"  "X110M_3.mdp_LEVEL"  
 [7] "X11117_6.mdp_LEVEL"  "X111M_5.mdp_LEVEL"   "X9617_2.mdp_LEVEL"  
[10] "X96M_1.mdp_LEVEL"    "X9717_8.mdp_LEVEL"   "X97M_7.mdp_LEVEL"   
[13] "X9817_10.mdp_LEVEL"  "X98M_9.mdp_LEVEL" 

> treenames <- treenames[c(4,6)]
> sub.rma<-Data.rma
> exprs(sub.rma, treenames) <- value
> str(sub.rma)

  ..@ treenames:List of 2
  .. ..$ : chr "X100M_11.mdp"
  .. ..$ : chr "X110M_3.mdp"


Regards,

Zhibin

> Date: Thu, 3 Jul 2008 21:58:38 +0200
> From: cstrato at aon.at
> To: zhbluweb at hotmail.com
> CC: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] subset in XPS
>
> 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
>>
>>
>

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