[BioC] [Rocky] - R code for PGSEA package to identify differentially expressed genes

[Valerie Obenchain]

On 01/25/12 21:12, Valerie Obenchain wrote:
> Hi Rocky,
>
> gsub() "finds and replaces". In this example we replace the dot with 
> an underscore. The double backslash in front of the dot is "escaping" 
> the dot because it is a special character (metacharacter). See ?regex 
> and ?gsub for details.
>
>     gsub("\\.", "A", c("foo.bar", ".foo"))
sorry, changed my example ... this should have been

gsub("\\.", "_", c("foo.bar", ".foo"))
>
> In the line you have below there are two gsub() statements. We can 
> rewrite the statement in pieces,
>
>     p <- phenoData(gse[[1]])$"characteristics_ch1"
>     x <- gsub("subtype: ", "", p)
>     subtype <- gsub("\\.", "_", x)
>
> Take a look at the output of each of these steps to better understand 
> what is going on.
>
> I don't understand the second part of your question, re: GSE11024. 
> What have you tried? Are you getting an error?
>
>
> Valerie
>
>
>
>
>
>
> On 01/24/12 23:01, haojam wrote:
>> Bioconductor Group,
>>
>>
>>
>> Hi,
>>
>> I have a special request regarding PGSEA Package to identify 
>> downregulated
>> genes. I am not clear about this line
>> subtype<- gsub("\\.", "_",gsub("subtype: ", "",
>> phenoData(gse[[1]])$"characteristics_ch1"))
>>
>> What does gsub ( ) mean for and \\ . I would like to look for GSE11024
>> having 5 subtypes and 0ne normal group, how could I proceed.
>>
>>
>>
>> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11024
>> GSM278765 - GSM278774 (10 samples) ->  CC_KIDNEY
>> GSM278775 - GSM278780 (6 samples) ->  CHR_KIDNEY
>> GSM278781 - GSM278792 (12 samples) ->  NOR_KIDNEY
>> GSM278793 - GSM278799 (7 samples) ->  ON_KIDNEY
>> GSM278800 - GSM278816 (17 samples) ->  Pappilary_KIDNEY
>> GSM278817 - GSM278843 (27 samples) ->  WM_KIDNEY
>>
>>
>>
>> Warm regards,
>>
>> Rocky
>>
>> SNU College of Medicine
>>
>> Korea
>>
>>
>>     [[alternative HTML version deleted]]
>>
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>
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