Hi All,
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
access controlled
i used commands tcgabiolinks
i used command GDC query
GDC download(query)
GDC prepare
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
Thank You
regards
ugandhar
If you are intending to get data from the Affy SNP 6.0 array, you should note that this is genotype data, not expression data. So if you want to do differential expression you need a different array platform.