[Rocky] - R code for PGSEA package to identify differentially expressed genes
0
0
Entering edit mode
@valerie-obenchain-4275
Last seen 2.8 years ago
United States
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 GO affy limma GLAD PGSEA GSEABase • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 939 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6