[BioC] accessing decideTests Info

Jason Skelton jps at sanger.ac.uk
Fri Nov 12 17:50:48 CET 2004


Hi all

I have the following data that I'd like to further explore
from decideTests
> summary(DTresults)
   Germball Cerc TwoDay SevenDay TwentyOneDay AdultWorm Egg
-1 1035      868  764    561      706          415       826
0  4891     5057 5144   5520     5178         5573      5150
1   602      603  620    447      644          540       552

I'd like to access particular parts of the tests results and was wondering if there was an easy way of doing this ?
There are seven treatments (Germball, cerc etc)

I'd like to create lists of genes from uniquegenelist
that are:
only downregulated in all treatments
only upregulated in all treatments
only up/down in one specific treatment or a couple of treatments 

Is this possible ? using grep or likewise ?
If so could someone show me an example please ?
I know that by looking at the results directly

e.g.
Germball Cerc TwoDay SevenDay TwentyOneDay AdultWorm Egg
[1,]        0    0      0        0            0         0   0
[2,]       -1    1      0        0           -1         0   0
[3,]        0    1      0       -1            0         0   1
[4,]        0    0      0        0            0         0   0
[5,]        0    0      0        0            0         0   0
6523 more rows ...

You have the gene information or can apply a unique genelist to it
Is this atall possible ?  

Many thanks for any help or advice

Jason

--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919



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