[BioC] where to start?
sdavis2 at mail.nih.gov
Wed Apr 20 15:22:03 CEST 2005
On Apr 20, 2005, at 12:06 PM, Malik Yousef wrote:
> 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
> samples. The samples define 32 phenotypes (classes). I would like to
> the significant genes among 10 different combinations of classes and
> 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
> the image format (or I'm missing some thing here). I want to read the
> 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
> table as fellow:
> GenId GeneName Sample1 Sample2 Sample3 Sample4 Sample5
> Class C1 C1 C2 C3 C4 C1
> 1 gene1 0.04 0.05 0.06 0.7 0.8 .......
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
You will probably benefit from reading:
> Where the second row have the class labels, and then at the third row
> 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
> So again I want to know how to read this file to the package???
For specific help on a function, type something like:
For searching for help on a specific topic, you can try:
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.
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