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

[Valerie Obenchain]

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"))

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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