I am attempting to import a file that I previously downloaded from GEO using the getGEO() function, howeer each time I try the function with my file name, I am met with an error that reads the following:
geo.getGEO.data <- getGEO(filename='GSE42394_series_matrix.txt')
# Rows: 29214 Columns: 25
# -- Column specification ------------------------------------------------------------
# Delimiter: "\t"
# dbl (25): ID_REF, GSM1150937, GSM1150938, GSM1150939, GSM1150940, GSM1150941, GS...
#
# i Use `spec()` to retrieve the full column specification for this data.
# i Specify the column types or set `show_col_types = FALSE` to quiet this message.
# File stored at:
# C:\Users\eemcn\AppData\Local\Temp\RtmpmkWS7R/GPL6247.soft
# Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
I have installed GEOquery using Bioconductor. My Biocrates was out of date so I had to update it, then I had to force reinstall GEOquery after receiving an error that read the following:
BiocManager::install("GEOquery")
# 'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
#
# replacement repositories:
# CRAN: https://cran.rstudio.com/
#
# Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
# Warning message:
# package(s) not installed when version(s) same as current; use `force = TRUE` to
# re-install: 'GEOquery'
BiocManager::install("GEOquery", force = TRUE)
# 'getOption("repos")' replaces Bioconductor standard repositories, see
# '?repositories' for details
#
# replacement repositories:
# CRAN: https://cran.rstudio.com/
#
# Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
# Installing package(s) 'GEOquery'
# trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/GEOquery_2.60.0.zip'
# Content type 'application/zip' length 13938121 bytes (13.3 MB)
# downloaded 13.3 MB
#
# package ‘GEOquery’ successfully unpacked and MD5 sums checked
Everything else is up-to-date. I have tried running this code as am Administrator as well. I'm happy to share the provided data file if that's helpful.
This is for a homework assignment, so as much as I appreciate ideas of other ways to load in this file, I need to use the getGEO() function to load in my data file for submission of this assignment. Thanks!