Question: arrayExpress: problem running code from the vignette
0
gravatar for kevin.rue
3.5 years ago by
kevin.rue230
University of Oxford
kevin.rue230 wrote:

Dear all,

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

... (truncated)

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))

Kind regards

Kevin

arrayexpress • 631 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by kevin.rue230
Answer: arrayExpress: problem running code from the vignette
0
gravatar for ugis
3.5 years ago by
ugis20
United Kingdom
ugis20 wrote:

Dear Kevin,

Thanks for pointing out the problem with queryAE, we'll check what is going on. However, since you mention that you are interested in RNA-seq datasets - the ArrayExpress package will be useful only for microarray data, see the description of the package:

"Access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet"

Best,

Ugis

 

 

 

ADD COMMENTlink written 3.5 years ago by ugis20

Hehehe.. the hint is in the name indeed ^^

I just got little confused as the 1000 genomes RNA-seq is linked from ArrayExpress (http://www.1000genomes.org/category/rnaseq/ and http://www.ebi.ac.uk/arrayexpress/experiments/E-GEUV-1/samples/), although indeed the files are physically hosted on the SRA.

Best,
Kevin

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by kevin.rue230

Hi Ugis, I am getting the same error message for queryAE as above. I am running R 3.3.1 with ArrayExpress 1.3.4 on Ubuntu 64bit. I've tried debugging the code and the issue occurs with this line:

  query = try(download.file(qr, queryfilename, mode = "wb"))

Any thoughts on how it could be fixed?

Thanks very much in advance

ADD REPLYlink written 3.0 years ago by meicaljohnjones0

Hi,

We cannot replicate the problem - it could be that there was a problem with ArrayExpress at the time. Could you try again please?

Best,

Ugis

ADD REPLYlink written 3.0 years ago by ugis20

Thanks so much for the prompt response, it's strange...it works for me with R console but not in rstudio. I'm guessing it's a character encoding thing.

ADD REPLYlink written 3.0 years ago by meicaljohnjones0
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