Question

Regarding ArrayExpress package

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akanksha17arora • 0

@akanksha17arora-24227

Last seen 4.2 years ago

Hello, I am trying to create an object for the Array Express processed data using ArrayExpress package. I did the following -

data<- getAE("E-MTAB-8871", type = "processed")
cname<- getcolproc(data)
show(cname)
AE<- procset(data, cname[2])

And I am getting the following error - 
**ArrayExpress: Reading pheno data from SDRF
Error in eval(substitute(expr), data, enclos = parent.frame()) : 
  Unable to read processed data**

I cannot figure out my mistake. Please help! Akanksha

microarray arrayexpress • 1.4k views

ADD COMMENT • link updated 4.2 years ago by James W. MacDonald 67k • written 4.2 years ago by akanksha17arora • 0

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I reproduced your error. The procset code is difficult to debug. Have you tried contacting the maintainer? It could be a problem with the archived data that the maintainer would see how to deal with. You should follow the posting guide and give the result of sessionInfo() when you contact the maintainer.

ADD REPLY • link 4.2 years ago Vincent J. Carey, Jr. 6.7k

score 0 · Answer 1 · 2020-09-29

Hi Akansha,

I understand you are accessing experiment E-MTAB-8871 from ArrayExpress that is associated Array design that we don't support(https://www.ebi.ac.uk/arrayexpress/arrays/A-MTAB-668/?ref=E-MTAB-8871). Our package at present does not support this technology as we don't anticipate to add this in the near future. We support following technologies at present for example such as “affymetrix”,”agilent","arrayvision","bluefuse","genepix","bluefuse","imagene","quantarray"

Thank you for using ArrayExpress.

All the best,

Suhaib