GEOquery: unable to fetch raw CEL files

Question

[prasad.chaskar]

Dear all,

I tried to access the raw data using getGEOSuppFiles (), but the untar () function did not return the necessary CEL files.

Code used:

###########
getGEOSuppFiles("GSE59857")
setwd("./GSE59857/")
untar("GSE59857_RAW.tar")
###########

untar returned only the platform files:

> dir()
[1] "GPL10558_HumanHT-12_V4_0_R1_15002873_B.txt.gz"
[2] "GPL10558_HumanHT-12_V4_0_R2_15002873_B.txt.gz"

I verified the successful download of the "GSE59857_RAW.tar" file.

R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

I appreciate any help in this regard.

Thanks

Answer 1

[Barry Digby]

As far as I can tell, the CEL files are not available on GEO, nor does the series exist on ArrayExpress...

Try downloading GSE59857_non-normalized.txt.gz and process it as per this post

[prasad.chaskar]

Thanks a lot Barry for your help.