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Question: Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages

1

15 months ago by

arbet003 • 10 wrote:

I am trying to load gene expression and phenotype data into R from a particular study that can be accessed at the GEO database (id: GSE72680) or at the ArrayExpress database (id: E-GEOD-72680). I have tried using both the GEOquery and ArrayExpress R packages to load this data into R but have been unsuccessful. I am wondering if anyone could help show me how to load the gene expression and phenotype data from this study into R. Thanks!

geneexpression geoquery arrayexpress • 356 views

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modified 15 months ago by Sean Davis ♦ 21k • written 15 months ago by arbet003 • 10

Looks like this submission contains no processed data from the submitter.

ADD REPLY • link modified 15 months ago • written 15 months ago by Sean Davis ♦ 21k

For GEOquery, I tried the following:

gdata <- getGEO('GSE72680', destdir=".")
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72680/matrix/
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version

I also tried setting GSEMatrix = F, and then tried following the advice here for converting the GSE files to an expressionset but that did not work.
I also tried loading the SOFT files directly into R:
gdata <-getGEO(filename='GSE72680_family.soft.gz')
but then I do not know how to extract the gene expression and phenotype data... again the problem is that I do not know how to convert the GSE files to an expressionset, the tutorial I linked above does not work.

For ArrayExpress, I tried the following:

data=ArrayExpress("E-GEOD-72680").... this doesnt work, says no raw data is available
data = getAE("E-GEOD-72680", type = "processed") cn = getcolproc(data) show(cn)

but this also doesnt appear to work, i.e. I the cn object doesnt contain anything, so I cant create the processed data using procset(data,cn[2])

ADD REPLY • link modified 15 months ago • written 15 months ago by arbet003 • 10

You'll need to update R and GEOquery. That SSL error is due to a change at NCBI that has been addressed in recent GEOquery versions. As for ArrayExpress, there is no "processed" data, so that approach won't work. See my answer below.

ADD REPLY • link written 15 months ago by Sean Davis ♦ 21k

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