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

Question

[selvasvce]

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

[Benn]

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

[russhh]

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

[Ram]

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

[selvasvce]

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.

[Ram]

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.

[selvasvce]

Sorry about that. I will take note of it.

Thank you :)