[BioC] How to read in log2 ratio data

[James W. MacDonald]

Hi Peter,

On 4/6/2011 4:25 AM, Peter Davidsen wrote:
> Hi all,
>
> I would like to conduct a time-course analysis using the limma package on my
> chip data (run as dual-color). I have two classes/groups with 8 subjects in
> each. Each 'experimental unit' has been measured at three different time
> points.
> However, I already have all the data as lowess normalized log-ratios =>
> log2(Hy3/Hy5).  How do I read in my txt-file with my log2 ratio data into R?
> And how do I define a vector/data frame?

This isn't a Bioconductor question. In fact, it isn't really an R-help 
question. I think you would be either ignored or eviscerated if you 
asked that over there.

If you don't know how to read data in, you are a fair bit from being 
able to do a time course analysis.

I would highly suggest you take the time to read 'An Introduction to R', 
so you can get past the data-manipulation steps.

http://cran.r-project.org/doc/manuals/R-intro.html

Best,

Jim


>
> I have arranged the data  so I have probe ID in the first column (row 2 to
> 200) and individual slide data in the following columns (that is, slide 1
> data in column 2, and slide 2 data in column 3 and so on...). I have 48
> slides in total.
>
> The main question I want to answer is which genes are differentially
> expressed between the two groups of subjects - at time point 1, 2, and 3,
> respectively.
>
> Cheers,
> Peter
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues