query to download Affymetrix HT_HG-U133A RMA level2 data

[veroniquevoisin]

query_microarray <- GDCquery(project = "TCGA-OV",
data.category = "Raw microarray data",
data.type = "Normalized intensities",
platform = "HT_HG-U133A",
access = "open",
legacy = TRUE)
GDCdownload(query_microarray )

RMA normalized are recommended over MAS5.0 level3 data

[risserlin]

Hi Veronique,
Thanks for the fix. the original data was downloaded directly from TCGA and it was RMA normalized so the protocol didn't use this method thankfully (although the microarray got cut altogether).
Do you have a link in the documentation where this is outlined so I can put the reference in the code as well.
Thanks,
Ruth