[BioC] where to start?

[Sean Davis]

On Apr 20, 2005, at 12:06 PM, Malik Yousef wrote:

> Hello,
> I have data that been preprocessed to have the gene expression for each
> genes, where I have 19200 genes involved in the experiments and I have  
> 186
> samples. The samples define 32 phenotypes (classes). I would like to  
> find
> the significant genes among 10 different combinations of classes and  
> then
> find out the intersection between those lists of significant genes.
>
> My problem was is how to read this simple data to any package of
> bioconductor, since I saw that bioconductor input format is more  
> requiring
> the image format (or I'm missing some thing here). I want to read the  
> input
> file where I want to keep track of the gene Id and the gene name.
> So please only provide me with simple example reading this input  
> format to
> any basic package of bioconductor. For simplicit consider that we have  
> a
> table as fellow:
> GenId GeneName   Sample1   Sample2  Sample3  Sample4 Sample5  
> ......SampleN
> Class            C1         C1       C2       C3      C4            C1
> 1       gene1    0.04       0.05     0.06     0.7     0.8  .......    
> 0.9
>

You can look at read.table for reading your file.  You may need to make  
some adjustments to your file, though, as read.table reads  
tab-delimited data.  As Michael pointed out in another message earlier,  
you will really benefit from using the original image files if you have  
them.

You will probably benefit from reading:

http://cran.r-project.org/doc/manuals/R-data.html#Spreadsheet_002dlike- 
data


> Where the second row have the class labels, and then at the third row  
> we
> have the gene expressions (just numbers!!).
>
> So I want to read this format to a specific bioconductor package (say
> limma/?) and start applying diffirent functions.

Have you read the limma user guide?  You will probably need to so that  
you can determine how to manipulate your data into a format that limma  
understands.

>
> So again I want to know how to read this file to the package???
>

For specific help on a function, type something like:

?read.table

For searching for help on a specific topic, you can try:

help.search('topic')

Unfortunately, a big part of using R and bioconductor is data  
manipulation (moving from one format to another), which will require  
learning some basic skills in R.  The Introduction to R manual is quite  
helpful.  Reading at least part of it and going through the examples it  
provides is pretty much necessary.

Hope this helps a bit.

Sean