So my actual gene list and sample list is longer (I can email you it if you would like but it is in the sam format as my posted code). From the download I get:
> query.exp <- GDCquery(project = "TCGA-HNSC",
+ legacy = TRUE,
+ data.category = "Gene expression",
+ data.type = "Gene expression quantification",
+ platform = "Illumina HiSeq",
+ file.type = "results",
+ experimental.strategy = "RNA-Seq",
+ barcode = samples)
Accessing GDC. This might take a while...
Of the 82 files for download 2 already exist.
We will download only those that are missing ones.
GDCdownload will download 80 files. A total of 121.269906 MB
Downloading as: Fri_Nov_11_13_53_28_2016.tar.gz
|======================================================================| 100%tar: Unrecognized archive format
tar: Error exit delayed from previous errors.
query.exp$results looks normal (I'm just pasting in the top for space):
center.code center.name center.short_name
31 07 University of North Carolina UNC
65 07 University of North Carolina UNC
67 07 University of North Carolina UNC
68 07 University of North Carolina UNC
My session info :
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
attached base packages:
 stats graphics grDevices utils datasets methods base