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

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
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written by selvasvce • selvasvce

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

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written by Benn Benn

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

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written by russhh russhh

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.

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updated by Ram Ram • written by selvasvce • selvasvce

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.
code_formatting

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written by Ram Ram

Sorry about that. I will take note of it.

Thank you :)

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written by selvasvce • selvasvce

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