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I've installed GEOquery with

install.packages("BiocManager")
BiocManager::install("GEOquery")
library(GEOquery)

then I ran the command

GSE68808 <- getGEO("GSE68808")

but it resulted in..

Found 1 file(s)
GSE68808_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68808/matrix/GSE68808_series_matrix.txt.gz'
Content type 'application/x-gzip' length 4138819 bytes (3.9 MB)
downloaded 3.9 MB

error: 'C:\Users\(myname)\AppData\Local\Temp\RtmpUp5Sv7\file8e844a7a59bc' does not exist.

ㅜㅜ

How can I solve this? thanks.

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  • $\begingroup$ Please consider accepting the answer if it has answered your question $\endgroup$
    – M__
    Commented Sep 15, 2023 at 20:22

1 Answer 1

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There seems to be some problem with your "platform specific tempdir" that is used by getGEO's destdir parameter. See ?getGEO for more info on the destdir parameter.

Try

GSE68808 <- getGEO("GSE68808", destdir = getwd())
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