tcgabioloink level 1 data

Question

[ugandhar.ch1]

Hi All,

i am using R and Bio conductor to analyze tcga-brca raw microarray data. i am using tcgabioloiks package for do this i am using GDC query, gdc download and GDC prepare to downolad data. i am successfully download data and placed it in working directory. but i am not getting expression set after gdc prepare command. i am not sure what step should i follow after gdc prepare for further analysis? my final aim is to get differential gene expression values. please help me

Thank you

regards ugandhar

Answer 1

[Mike]

Could you please post your initial code, so it would be easy for others to find out your error.