GEO RNASeq data query
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20yx17 ▴ 10
@07f7a8c7
Last seen 9 days ago
Canada

Hi,

I am trying to query RNA seq datasets (GSE117271 and GSE117403) by using the GEOquery package, but it doesn't work.

The code is here. It works for microarray data rather than this RNA seq data:

 GSE117271 <- getGEO(GEO = "GSE117271",
                     destdir = "GEO sets",
                     AnnotGPL = T)

The error:

Annotation GPL not available, so will use submitter GPL instead Using locally cached version of GPL18573 found here: GEO sets/GPL18573.soft  

Warning message:  In download.file(myurl, destfile, mode = mode, quiet
= TRUE, method = getOption("download.file.method.GEOquery")) :   cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL18nnn/GPL18573/annot/GPL18573.annot.gz': HTTP status was '404 Not Found'

GEO help desk told me that

GSE117271 and GSE117403 contain sequencing data (and not microarray data). Such studies do not have Sample data tables, and so the GEO Series Matrix Files (which are downloaded by GEOquery) do not have processed data.

Is this why it doesn't work? Or the arguments should be changed? Are there other functions or packages to query such RNA seq data in R?

Thank you in advance for your help and ideas!

GEOquery RNASeq GEO • 121 views
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That is a warning, not an error, so I suspect that GSE117271 now contains the sample and study metadata, but no expression values.

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@james-w-macdonald-5106
Last seen 22 hours ago
United States

Yes, that is why it doesn't work. You could try the SRAdb package, or the NCBI toolkit. But do note that you will be getting the actual reads if you do that, and you will then need to align to the genome.

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