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

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