System biology help for cancer data base analysis to check altered genes.

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6.3 years ago

selvasvce ▴ 10

Dear ALL, It is going to be some important questions. Can anyone help me with R programming for downloading the cancer data from cBioportal. I need to perform Differential gene expression analysis in Breast cancer from cBioportal , TCGA DATABASE. Please, it will be great if I get some help from fellow system biology people.

Thanks again for your time.

Best Regards, Selva

RNA-Seq rna-seq next-gen gene R • 1.2k views

ADD COMMENT • link 6.3 years ago by selvasvce ▴ 10

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I think your question is too broad, or is this a job ad?

ADD REPLY • link 6.3 years ago by Benn 8.3k

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If you want help, show your code and how you have approached the problem

ADD REPLY • link 6.3 years ago by russhh 5.7k

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We have cleaned, R-ready TCGA data available for easy download here: http://linkedomics.org/login.php#dataSource

ADD REPLY • link 6.3 years ago by Ram 44k

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Hello all Thanks for the reply,(Beginner)

source("http://bioconductor.org/biocLite.R")
biocLite()
install.packages('cgdsr')
library(cgdsr)
mycgds <- CGDS("http://www.cbioportal.org/public-portal/")
getCancerStudies(mycgds)
mycancerstudy = getCancerStudies(mycgds)
breast_study <- getCancerStudies(mycgds)[25,1]
pca_case_list <- getCaseLists(mycgds,breast_study)[1,1]

here is the code and I need to further proceed to check normalization and check for differential gene expression. Please help me in this thanks.

ADD REPLY • link updated 6.3 years ago by Ram 44k • written 6.3 years ago by selvasvce ▴ 10

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Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply instead. Also, please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
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