Question: can I extract data for subset of cancer types from GSE62944
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gravatar for richa_makhijani
2.5 years ago by
richa_makhijani0 wrote:

Hi, I am interested in extracting expression data for only three cancer types from GSE62944. I want tumor/normal integer based read counts for these cancers, from which I want to extract Differential expressed genes using LIMMA. Is it possible to do so? I am not able to understand which samples belong to which tumor types and how to extract them. Also, can it directly feed the feature counts data to LIMMA for differential expression?

limma rna-seq • 427 views
ADD COMMENTlink modified 2.5 years ago by sina.nassiri70 • written 2.5 years ago by richa_makhijani0
Answer: can I extract data for subset of cancer types from GSE62944
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gravatar for sina.nassiri
2.5 years ago by
sina.nassiri70
Switzerland/Lausanne
sina.nassiri70 wrote:

Have you read the vignette? https://github.com/Bioconductor/GSE62944/blob/master/vignettes/GSE62944.Rmd

There is an example on subsetting data for Low Grade Glioma (LGG), which you can easily modify for other cancer types.

# metadata on cancer types
phenoData(tcga_data)$CancerType

# subset the expression Set to only samples from LGG for example
lgg_data <- tcga_data[, which(phenoData(tcga_data)$CancerType=="LGG")]

The example continues with differential expression analysis using DESeq2, but you can also use limma. Check the following workflow on using limma for RNASeq: 

source("http://bioconductor.org/workflows.R")
workflowInstall("RNAseq123")

Hope this helps!

 

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by sina.nassiri70
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