[BioC] help with fit function
James W. MacDonald
jmacdon at med.umich.edu
Wed Sep 8 17:35:28 CEST 2010
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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