[BioC] Microarray data analysis

Gordon K Smyth smyth at wehi.EDU.AU
Tue Mar 25 02:28:10 CET 2014

The limma User's Guide includes a series of fully worked case studies 
starting in Chapter 16, and raw data is provided for all or most of them.

The earlier chapters describe how one would use code.  Readers are 
expected to adapt this advice to their own data and situation.

The code you give occurs on page 12, and immediately before it the text 

"This is a quick overview of what an analysis might look like. ... We 
assume that the images have been analyzed using GenePix to produce a .gpr 
file for each array and that a targets file targets.txt has been prepared 
with a column containing the names of the .gpr files."

This tells you that it is a hypothetical example.

Realistically, microarray data is quite complex, and you should expect to 
have to read further than the second page of the "quick start" before 
knowing enough to do an analysis for yourself.

Best wishes

> Date: Sun, 23 Mar 2014 21:40:41 +0800 (SGT)
> From: prabhakar ghorpade <prabhakar_ghorpade at yahoo.co.in>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: Re: [BioC] Microarray data analysis
> Hello, 
> Thanks for reply.  I am trying to run limma with user guide instructions but from page 11 of user guide. I am getting following error
>> targets <- readTargets("targets.txt")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>   cannot open file 'targets.txt': No such file or directory
>  How can I proceed with it? Did I need target.txt file of my own or does limma has example file in its package? 
> Dr. Ghorpade Prabhakar B.
> PhD Scholar ( Veterinary Biochemistry),
> Izatnagar,
> Bareilly, U.P.,
> India
> On Saturday, 22 March 2014 11:43 PM, Levi Waldron <levi.waldron at hunter.cuny.edu> wrote:
>> From the http://www.bioconductor.org/help/ page, check out the "Oligonucleotide arrays" link which has example data and workflows.
> On Sat, Mar 22, 2014 at 11:22 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> For microarray data analysis, I would starting with the limma package.  The
>> User Guide is a great resource, so I would suggest reading sections of it
>> to get you going.
>> Sean
>> On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade <
>> prabhakar_ghorpade at yahoo.co.in> wrote:
>>> Hi Friends,
>>>    I want to use Bioconductor for microarray data analysis for that I need
>>> one example data on which I can try R codes? Can you please suggest start
>>> point for learning Bioconductor. Which package I should start with? Thanks.

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