How to get data from GEO by using getGEO function ?

0

Entering edit mode

4.1 years ago

11818480 • 0

Hello everyone,

I am using R package GEOquery to get a geo object from file ( in my directory) by getgeo function. I already download the required packages

BiocManager::install("DESeq2")
BiocManager::install("limma")
BiocManager::install("GEOquery")

library(DESeq2)
library(limma)
library(Biobase)
library(GEOquery)

I used this code and get this message

getGEO("GPL96.annot.txt.gz")

Using locally cached version of GPL96.ANNOT.TXT.GZ found here:
C:\Users\MTECH~1\AppData\Local\Temp\RtmpsHinCo/GPL96.ANNOT.TXT.GZ.soft 
Error in parseGSEMatrix(fname, destdir = destdir, AnnotGPL = AnnotGPL,  : 
  parsing failed--expected only one '!series_data_table_begin'

could anyone help me because I am beginner in R , please ?

RNA-Seq R • 2.5k views

ADD COMMENT • link updated 2.7 years ago by yuanyuan • 0 • written 4.1 years ago by 11818480 • 0

0

Entering edit mode

GEO A character string representing a GEO object for download and parsing. (eg., 'GDS505','GSE2','GSM2','GPL96')

Can you try:

getGEO("GPL96")