i just met a warning below when i tried to run these code:

options(stringsAsFactors = F)
> f='GSE154851_eSet.Rdata'
> 
> library(GEOquery)
> #Setting options('download.file.method.GEOquery'='auto')
> #Setting options('GEOquery.inmemory.gpl'=FALSE)
> if(!file.exists(f)){
+     gset <- getGEO('GSE154851', destdir=".",
+                    AnnotGPL = F,     
+                    getGPL = F)       
+     save(gset,file=f)   
+ }

the warning:

Warning: 1 parsing failure.
 row col   expected     actual                               file
1672  -- 71 columns 48 columns './GSE154851_series_matrix.txt.gz'

MY question is: what does it mean?(Does it mean that the result is not available for next-step analysis?) How can I solve it?

ttttttthanks for your Time!!!!!

Sheldon

If you are trying to download GSE154851 data on your machine, I just performed gset <- getGEO('GSE154851', destdir=".",AnnotGPL = F, getGPL = F) and I didn't get any error message, I think you could do the same