i am using R and Bio conductor for analyzing TCGA controlled data BRCA.
data category raw microarray
data type raw intensities
platform Affymetrix SNP Array 6.0
i used commands tcgabiolinks
i used command GDC query
i am not sure what should i do after this step?
my final aim to do differential expression?
what package should i use?
what prompt i get after GDC prepare? i think i should get expression set, but i am not getting it
tcga data is downloaded and placed in working directory
please help me.. i am not finding any source for help