[BioC] subset in XPS

[cstrato]

Dear Zhibin

This is strange, I will investigate.

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
>
>   
>> Date: Mon, 30 Jun 2008 21:29:23 +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
>>
>> Meanwhile, I have uploaded a new version to BioC devel:
>> http://bioconductor.org/packages/2.3/bioc/html/xps.html
>> which simplifies your request as follows:
>>
>> 1. get expression values
>>     
>>> value <- exprs(data.rma)
>>>       
>> 2. select treenames of choice (no extension necessary)
>>     
>>> treenames <- c("TestA2", "TestB1")
>>>       
>> 3. make a copy of your object if you do not want to replace it
>>     
>>> sub.rma <- data.rma
>>>       
>> 4. replace slot data with subset
>> exprs(sub.rma, treenames) <- value
>> 5. check if the new ExprTreeSet is correct:
>>     
>>> str(sub.rma)
>>>       
>> Best regards
>> Christian
>>
>>
>> Zhibin Lu wrote:
>>     
>>> Dear Christian,
>>>
>>> Thanks so much for such a detailed explanation. I will try this when I
>>> get to work next week, and I do not see why I can not follow the
>>> direction.
>>>
>>> Thanks again and have a nice weekend,
>>>
>>> Zhibin
>>>
>>>       
>>>> Date: Sat, 28 Jun 2008 15:46:26 +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
>>>>
>>>> Since you have already done RMA you have now an ExprTreeSet,
>>>> called e.g. "data.rma". You can see the structure with:
>>>>         
>>>>> str(data.rma)
>>>>>           
>>>> Since currently there is no direct possibility to use a
>>>> subset of type ExprTreeSet only, you can create a new class
>>>> ExprTreeSet in the following way:
>>>>
>>>> 1. Make a subset of slot "data" which is a dataframe
>>>> (assuming that you want to use samples 1,2,3,7,8,9):
>>>>         
>>>>> subdata <- exprs(data.rma)
>>>>> subdata <- subdata[,c(1:2,3:5, 9:11)]
>>>>>           
>>>> Please note that it is important to keep the first
>>>> two columns.
>>>>
>>>> 2. Create a copy "sub.rma" of class "data.rma"
>>>>         
>>>>> sub.rma <- data.rma
>>>>>           
>>>> 3. Replace slot "data" with "subdata":
>>>>         
>>>>> exprs(sub.rma) <- subdata
>>>>>           
>>>> For the moment you need to replace slots "treenames" and
>>>> "numtrees", too, which I will change in the future to be
>>>> done automatically.
>>>>
>>>> 4. Replace slot "treenames" with the names of your subset:
>>>> a, create list containing the sub samples
>>>>         
>>>>> subtrees <- unlist(treeNames(data.g.rma))
>>>>> subtrees <- as.list(subtrees[c(1:3,7:9)])
>>>>>           
>>>> b, check if the names are correct:
>>>>         
>>>>> subtrees
>>>>>           
>>>> c, replace slot "treenames":
>>>>         
>>>>> sub.rma at treenames <- subtrees
>>>>>           
>>>> 5. Replace slot "numtrees" with the number of subsamples
>>>>         
>>>>> sub.rma at numtrees <- length(subtrees)
>>>>>           
>>>> 6. Check if the new ExprTreeSet is correct:
>>>>         
>>>>> str(sub.rma)
>>>>>           
>>>> Now you can use the new ExprTreeSet "sub.rma" as input for
>>>> method unifilter:
>>>>         
>>>>> rma.ufr <- unifilter(sub.rma, .......)
>>>>>           
>>>> If you want to take advantage of the advanced capabilties
>>>> of package "limma", then you can create a Biobase class
>>>> "ExpressionSet" containing only your 6 samples as described
>>>> in Appendix A.3 of the vignette xps.pdf:
>>>>
>>>> 1. extract the normalized expression data:
>>>>         
>>>>> subdata <- validData(data.rma)
>>>>>           
>>>> 2. Since "subdata" is a dataframe, simply create a subframe:
>>>>         
>>>>> subdata <- subdata[,c(1:3,7:9)]
>>>>>           
>>>> 3. Create a Biobase class "ExpressionSet", called "subset"
>>>>         
>>>>> subset <- new("ExpressionSet", exprs = as.matrix(subdata))
>>>>>           
>>>> Now you have an ExpressionSet ready for use with "limma".
>>>>
>>>> Please let me know if you succeeded with this info.
>>>>
>>>> Best regards
>>>> Christian
>>>> _._._._._._._._._._._._._._._._
>>>> C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>>> V.i.e.n.n.a A.u.s.t.r.i.a
>>>> e.m.a.i.l: cstrato at aon.at
>>>> _._._._._._._._._._._._._._._._
>>>>
>>>> Zhibin Lu wrote:
>>>>         
>>>>> Hi,
>>>>>
>>>>> I am new in R/bioconductor. I am using xps package to analyze
>>>>>           
>>> Affymetrix Gene ST 1.0 data. After I loaded CEL files into the
>>> DataTreeSet and compute the expression level with RMA, can I work on a
>>> subset of the data? Say, I have 12 samples. After RMA, can I just work
>>> on 6 of them and divide them into two groups and apply UniFilter to
>>> just these 6 ones?
>>>       
>>>>> Thanks,
>>>>>
>>>>> Zhibin
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>>           
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>       
>>>>>
>>>>>           
>>> ------------------------------------------------------------------------
>>>       
>
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