rbioinformatics

Failed to load expression data from Geodataset in R


I'm new to Bioinformatics and have been stuck on this since last week. The problem is that I can't load up the expression data and have tried everything possible. The accession ID of this data is "GSE244858". Please your assistance will be much appreciated. Thank you in advance

I need to get the expression data and analyze it, But keeps showing the list of samples instead of the expression data

gse<- getGEO("GSE244858", GSEMatrix = TRUE)
Found 1 file(s)
GSE244858_series_matrix.txt.gz
Using locally cached version: C:\Users\hp\AppData\Local\Temp\Rtmp8i5Jzt/GSE244858_series_matrix.txt.gz
Using locally cached version of GPL24247 found here:
C:\Users\hp\AppData\Local\Temp\Rtmp8i5Jzt/GPL24247.soft.gz 
> length(gse)
[1] 1
> gse <- gse[[1]]
> exprs(gse)
     GSM7830913 GSM7830914 GSM7830915 GSM7830916 GSM7830917 GSM7830918 GSM7830919
     GSM7830920 GSM7830921

Solution

  • It's RNA-seq, not microarray. getGEO only supports arrays. But at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE244858 at the bottom there seems to be the expression values as a supplemental file.