[BioC] How to create a MAList or ExprSet object from a matrix

[Francois Pepin]

Hi Shiliang,

As a note, I would point out that your data are almost certainly not
expression ratio (although they do look like log2 values). Affy chips
give absolute intensity levels, as opposed to the ratios that one
generally gets from two-color arrays.

The expression ratio (M values) would centered around 0 for the majority
of genes which are not differentially expressed.

The steps that Martin Morgan gave you to create exprSet give you the
object you want, but you should really try to make sure that you
understand properly what your data is. Otherwise, you will likely have
serious problems interpreting the results at the end.

Francois

On Tue, 2006-08-15 at 14:07 -0400, swang wrote:
> Dear List:
> 
> I got a file like the following, I guess the data is M ( log2 expression
> ratio) from microarray:
> 
>     56071 1052 1062 3061 3081 8052 8072 10061 10062 10072 1415670_at
> 8.430148 8.899385 8.625973 8.708319 8.759182 8.281378 8.905347 8.625347
> 9.029528 1415671_at 9.039655 9.244914 9.121714 9.002296 8.97237 8.599152
> 9.004381 9.267188 9.115415 1415672_at 8.86041 8.998826 9.077138 8.994297
> 8.885136 8.918512 9.087072 8.867808 8.841663 1415673_at 6.565344 6.384893
> 6.856466 6.17951 5.786523 6.507357 6.371563 5.886887 6.42499 1415674_a_at
> 7.877212 8.038635 8.120319 8.067843 7.56546 7.846677 7.921398 7.629843
> 7.787807 1415675_at 7.524559 7.496189 7.718928 7.164805 7.102158 7.331314
> 7.226036 7.424044 7.368011 1415676_a_at 9.315694 9.134394 9.224642 8.821193
> 8.886963 8.702572 8.883647 9.028728 8.921372
> 
> the rows are Affymetrix probe and columns are different mice number (arrays)
> I need to do a category analysis using category package, so I need to
> generate a MAList or ExprSet object.
> Is there anybody who can tell me how to do it?
> 
> thanks
> 
> Best
> 
> Shiliang
> 
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