I am trying to start some analysis of RNA seq data with R. However, I am having some trouble with downloading the data.
I have downloaded the following libraries:
install.packages("BiocManager") install.packages("forcats") install.packages("stringr") install.packages("ggplot2") install.packages("ggrepel") install.packages("readr") install.packages("tidyr") install.packages("survminer") BiocManager::install("GEOquery") BiocManager::install("limma") BiocManager::install("pheatmap") BiocManager::install("org.Hs.eg.db")
Ran this code:
library(GEOquery)
gse <- getGEO("GSE120575")
gse
But get this output:
gse <- getGEO("GSE120575") Found 1 file(s) GSE120575_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120575/matrix/GSE120575_series_matrix.txt.gz' Content type 'application/x-gzip' length 7022 bytes downloaded 7022 bytes
File stored at: C:\Users\lukej\AppData\Local\Temp\Rtmp8W0ANd/GPL18573.soft.gz Error in readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) : error reading from the connection In addition: Warning messages: 1: In for (getMethodName in getMethodNames) { : closing unused connection 3 (C:\Users\lukej\AppData\Local\Temp\Rtmp8W0ANd/GPL6947.soft.gz) 2: In readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) : invalid or incomplete compressed data
Can someone please advise?
