Question: [Rocky] - R code for PGSEA package to identify differentially expressed genes
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gravatar for Valerie Obenchain
7.6 years ago by
United States
Valerie Obenchain6.7k wrote:
Hi Rocky, I'm pasting your message here so we can keep all comments on the mailing list. ## --------------------------------------------------------------- Dear Valerie, I would like to find down-regulated expression signatures for each sample from GSE11024 dataset containing 79 samples. How could I implement using PGSEA to get it. I would be glad and highly appreciate for your kindness. 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 I also tried with affy and LIMMA package for normalizing the GSM CEL files using these code ? source("http://www.bioconductor.org/biocLite.R") biocLite("limma") biocLite("affy") library(affy) setwd("/home/haojamrocky/DATA/GSE11024") rawdata<-ReadAffy() eset <- expresso(rawdata, normalize.method="quantiles",bgcorrect.method="rma",pmcorrect.method=" pmonly",summary.method="liwong") write.exprs(eset, file="mydata.txt") Warm regards, Rocky ## --------------------------------------------------------------- Have you tried following the PGSEA workflow vignette? If yes, at what point do you get an error? The vignette says you need a gene expression dataset which I assume you downloaded from the ncbi site above. You also need a list of gene sets. Looking at the man page (?PGSEA) we see the PGSEA function requires the expression data to be a matrix, eset or ExpressionSet. Is your expression data in one of these forms? The gene list must be a GeneSetCollection or list of SMC objects. If you are having trouble creating your gene set see the vignettes in the GSEAbase, GO or GSEAlm packages. Valerie On 01/25/12 21:53, Valerie Obenchain wrote: > 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]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
go affy limma glad pgsea gseabase • 590 views
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