[BioC] plotting a CA

Aedin aedin at jimmy.harvard.edu
Sat Mar 10 15:28:18 CET 2012

Hi Aoife
Welcome to R. I understand it can seem tough at first. But you are learning a language that will be wonderful once you do. I find new users like the Rstudio.org interface to R 

Scan works easy for a one column file. It will read it in as a vector that you then have to convert to a factor. It's more complicated when you have >1 column

In that case you might find it easier to create an annotation file in excel. Save it as a csv  (comma delimited)  file  It can contain >1 column  eg a column of gene names and a second of categories etc. then use read.csv  to read it into R  Then select the column you want eg if it's the second column:

annot<~read.csv("file.csv", header=TRUE)

read.csv or read.table will read any categorical column as a factor by default. Use? To get help on a function. Or use help.search to search for a function. The website rseek.org is a good google like search engine for all things R 

There are several intro to R textbooks which might be useful to me   I can send you a list if you wish  Or look at Tom Girke UC riverside's  online class or i link course notes on an intro to R class I teach on my website. 

Good luck 

On Mar 10, 2012, at 5:50, aoife doherty <aoife.m.doherty at gmail.com> wrote:

> change

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