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: 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. -- ----------------------------------------------------- Dr. Alberto Goldoni Parma, Italy

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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues