I am trying to use the arrayExpress package following examples in the vignettes, however I cannot seem to query the ArrayExpress database with keywords. Nevertheless, it seems that downloading works fine. See below:
> queryAE(keywords = "pneumonia") downloaded 0 bytes Error in download.file(qr, queryfilename, mode = "wb") : cannot download all files In addition: Warning message: In download.file(qr, queryfilename, mode = "wb") : URL 'http://www.ebi.ac.uk/arrayexpress/xml/v2/experiments?keywords=pneumonia&species=': status was '400 Bad Request' Error: XML content does not seem to be XML: 'querypneumonia.xml'
However that works:
> getAE("E-MEXP-1422", type = "full") trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-AFFY-37/A-AFFY-37.adf.txt' Content type 'unknown' length 2442272 bytes (2.3 MB) ================================================== downloaded 2.3 MB
Note that both examples are copied from the corresponding vignettes. I am personally looking for whole-blood RNA-seq data sets.
EDIT: I am using ArrayExpress 1.32.0, which the nightly build reports successful (Snapshot Date: 2016-05-03 17:20:26 -0700 (Tue, 03 May 2016))