Hello, I need to extract this txt file. When I used following command line: Data_GPL5571 <- read.table('GSE27634-GPL5571_series_matrix.txt.gz') I got this error: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 46 did not have 2 elements Thanks, Jerry [[alternative HTML version deleted]]

On Thu, Feb 27, 2014 at 1:40 PM, Jerry Cholo <jerrycholo@gmail.com> wrote: > Hello, > > Hi, Jerry. > I need to extract this txt file. When I used following command line: > Data_GPL5571 <- read.table('GSE27634-GPL5571_series_matrix.txt.gz') > > First, I am curious where this file came from, as I don't think this came from NCBI GEO, judging from the metadata associated with GSE27634. I got this error: > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > line 46 did not have 2 elements > Second, read.table is for reading tabular data. The Series Matrix format is tabular, but it has a header that varies in the number of columns, so I would not expect read.table to work directly on a series matrix file. The error above arises from the fact that the number of columns is not 2 (is probably actually 1 column) at line 46. Your email is entitled getGEO, but you don't actually use GEOquery. Perhaps this is what you want? gse = getGEO('GSE27634')[[1]] Hope that helps. Sean [[alternative HTML version deleted]]