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You have not given any information on how you have used getGEO.  To help
you, I issued

> library(GEOquery)
Setting options('download.file.method.GEOquery'='auto')
> gg = getGEO("GDS157")
File stored at:
/var/folders/4D/4DI98FkjGzq0K2niUTEHSE+++TM/-Tmp-//RtmpGnz9Cf/GDS157.soft.gz
> gg
An object of class "GDS"
channel_count
[1] "1"
dataset_id
[1] "GDS157" "GDS157"
description
[1] "Analysis of gene expression in pooled vastus lateralis muscle samples
from insulin-sensitive and insulin-resistant equally obese, non-diabetic
Pima Indians. A search for susceptibility genes for type 2 diabetes.    "
...

> getClass("GDS")
Class "GDS" [package "GEOquery"]

Slots:

Name:           gpl    dataTable       header
Class:          GPL GEODataTable         list

Extends: "GEOData"
> getClass("GEODataTable")
Class "GEODataTable" [package "GEOquery"]

Slots:

Name:     columns      table
Class: data.frame data.frame

Here I am using R's self-describing capacities to learn about what the
query returned.

> gg@dataTable@columns
    sample        metabolism
1  GSM2289 insulin resistant
2  GSM2294 insulin resistant
3  GSM2299 insulin resistant
4  GSM2304 insulin resistant
5  GSM2309 insulin resistant
6  GSM2313 insulin sensitive
7  GSM2318 insulin sensitive
8  GSM2323 insulin sensitive
9  GSM2328 insulin sensitive
10 GSM2333 insulin sensitive

description
1  Value for GSM2289: insulin resistant sample pool 1 muscle on HuFL; src:
muscle
2  Value for GSM2294: insulin resistant sample pool 2 muscle on HuFL; src:
muscle
3  Value for GSM2299: insulin resistant sample pool 3 muscle on HuFL; src:
muscle
4  Value for GSM2304: insulin resistant sample pool 4 muscle on HuFL; src:
muscle
5  Value for GSM2309: insulin resistant sample pool 5 muscle on HuFL; src:
muscle
6  Value for GSM2313: insulin sensitive sample pool 1 muscle on HuFL; src:
muscle
7  Value for GSM2318: insulin sensitive sample pool 2 muscle on HuFL; src:
muscle
8  Value for GSM2323: insulin sensitive sample pool 3 muscle on HuFL; src:
muscle
9  Value for GSM2328: insulin sensitive sample pool 4 muscle on HuFL; src:
muscle
10 Value for GSM2333: insulin sensitive sample pool 5 muscle on HuFL; src:
muscle

Now I start to see that the collection of samples may be viewed as falling
into two classes.  If you want to use wilcox.test to address a two-sample
problem arising from this experiment, you will have to use the information
shown above to distinguish numerical values on gene expression into the
classes.  There is more than enough information in the above to begin this
process; for biological interpretation you need to know a little more: you
will need to know the GPL80 is documented in the package hu6800.db.

On Tue, Mar 20, 2012 at 7:24 AM, Ovokeraye Achinike-Oduaran <
ovokeraye@gmail.com> wrote:

> Hi all,
>
> I am not quite sure how to use the expression set I get from getGEO(),
> say gds157, in wilcox.test().
>
> Please help.
>
> Thanks.
>
> Avoks
>
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