Question

arrayExpress: problem running code from the vignette

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kevin.rue ▴ 350

@kevinrue-6757

Last seen 6 months ago

University of Oxford

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 • 2.1k views

ADD COMMENT • link 8.6 years ago kevin.rue ▴ 350

score 0 · Answer 1 · 2016-05-05

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ugis ▴ 20

@ugis-7915

Last seen 2.1 years ago

United Kingdom

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 COMMENT • link 8.6 years ago ugis ▴ 20

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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 REPLY • link 8.6 years ago kevin.rue ▴ 350

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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 REPLY • link 8.1 years ago meicaljohnjones • 0

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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 REPLY • link 8.1 years ago ugis ▴ 20

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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 REPLY • link 8.1 years ago meicaljohnjones • 0