[BioC] PreProcess and Limma 'done'. What directions now?

[Massimo Pinto]

Hi John,

On Wed, Jun 10, 2009 at 12:15 PM, john seers
(IFR)<john.seers at bbsrc.ac.uk> wrote:
>
> Hi Massimo
>
>>I have beem through normalization and basic limma operations.
>
> Does this mean you have extracted lists of genes using topTable? You can
> add your annotation to these lists of genes using the "genelist"
> parameter of topTable. Something like "genelist=cbind(fit$genes,
> mappings)". Assuming your mappings are in the same order as your fit
> data.
>

yes they seem so

> fit2.Cn.eb$genes[1:10,1]
 [1] "A_24_P66027"  "A_32_P77178"  "A_23_P212522" "A_24_P934473"
"A_24_P9671"   "A_24_P801451" "A_32_P30710"  "A_24_P704878"
"A_32_P86028"
[10] "A_23_P65830"

> mappings[1:10,1]
 [1] A_24_P66027  A_32_P77178  A_23_P212522 A_24_P934473 A_24_P9671
A_24_P801451 A_32_P30710  A_24_P704878 A_32_P86028  A_23_P65830
25574 Levels: A_23_P100001 A_23_P100011 A_23_P100022 A_23_P100074
A_23_P100092 A_23_P100103 A_23_P100111 A_23_P100127 ... A_32_P99933

therefore using your suggestion, topTable() nicely returns

> toptable(fit2.Cn.eb,genelist=cbind(mappings$DESCRIPTION, fit2.Cn.eb$genes), number=5)
                         mappings.DESCRIPTION           ID     logFC
      t      P.Value    adj.P.Val        B
14442 fatty acid binding protein 4, adipocyte   A_23_P8812 -3.055038
-17.02303 7.819269e-14 1.999700e-09 18.06843
15172         beta-site APP-cleaving enzyme 2  A_24_P14584 -2.287226
-15.25732 6.721762e-13 6.639688e-09 16.72509
8406            hypothetical protein MGC10981 A_32_P178092 -1.899104
-15.14233 7.788795e-13 6.639688e-09 16.62917
3390          beta-site APP-cleaving enzyme 2 A_23_P154875 -2.006084
-14.41987 2.009131e-12 1.284538e-08 16.00055
4688                          forkhead box N3 A_23_P140405 -1.175783
-13.22849 1.047477e-11 5.357635e-08 14.85805

>>What I would like to do here is to ask questions like "what happened to
> this
>>and that particular gene"?
>
> You can extract any gene you like from a topTable gene list. Along with
> the expression/p-values etc. You can extract the actual expression
> values using the Affymetrix probe name or your gene annotation name.
>

to tackle this I will look more closely into the suggestion written by
Vincent (whom I would like to thank here, for a start).
Thanks to you too.

Massimo

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