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

[Jenny Drnevich]

At 01:07 PM 8/15/2006, 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


These values are definitely not M values ( log2 expression ratio) - they 
are way too large and all positive. Given that there are Affymetrix 
probeset IDs, they are single channel intensity values, with one sample per 
array. Do you know what preprocessing was applied? Affymetrix arrays have 
multiple probes per probeset, but you have only one number per probeset, so 
they must have been preprocessed somehow, likely with Affy's MAS5 
algorithm. You should find out what was done, because likely background 
correction and normalization have already been applied, so you don't need 
to do those steps again.

Cheers,
Jenny





>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
>
>         [[alternative HTML version deleted]]
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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ph: 217-244-7355
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e-mail: drnevich at uiuc.edu