[BioC] help with fit function

[James W. MacDonald]

Hi Alberto,

On 9/8/2010 9:49 AM, Alberto Goldoni wrote:
> Dear All,
> thanks to the function: fit<- eBayes(fit) i can obtain the toptable like this:
>
>> topTable(fit,coef=2)
>        Row Col ProbeUID ControlType    ProbeName  GeneName SystematicName
> 5118   26  12     4558           1    (+)eQC-13       eQC            eQC
> 4520   23   1     4296           1    (+)eQC-02       eQC            eQC
> 6868   34  73     6435           0 A_42_P490236 409568_Rn      409568_Rn
> 4932   25  19     4381           1    (+)eQC-20       eQC            eQC
> 4729   24   2     4496           1    (+)eQC-03       eQC            eQC
> 4464   22 158     4240           0  A_43_P11468 NM_012571      NM_012571
> 4735   24  10     4502           1    (+)eQC-11       eQC            eQC
> 18777  92  42    17921           0 A_42_P781006 296921_Rn      296921_Rn
> 5110   26   4     4551           1    (+)eQC-05       eQC            eQC
> 4741   24  18     4508           1    (+)eQC-19       eQC            eQC
>
> but from the "fit" table i would like to obtain a new table without
> row in witch the value "fit$ControlType" would be "+1" and "-1".
> like this:

This is just simple data manipulation, having nothing to do with the fit 
function nor with limma in general.

out <- topTable(fit, coef=2)
out[out$ControlType == 0,]

If you are struggling with these sorts of rudimentary data manipulation, 
I would highly recommend reading 'An Introduction to R', which comes 
with R, and can also be found here:

http://cran.r-project.org/doc/manuals/R-intro.html

Best,

Jim
>
>        Row Col ProbeUID ControlType    ProbeName  GeneName SystematicName
> 6868   34  73     6435           0 A_42_P490236 409568_Rn      409568_Rn
> 4464   22 158     4240           0  A_43_P11468 NM_012571      NM_012571
> 18777  92  42    17921           0 A_42_P781006 296921_Rn      296921_Rn
>
> is it possible, somebody can help me?
>
> Best regards.
>
>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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