[R] Help On EBAM

From: Learning R <learningr_at_gmail.com>
Date: Thu 14 Sep 2006 - 19:04:11 GMT


Dear RUsers,

I am new to R. I am learning how to use R. I am a PC user and run R on windows. I would appreciate if some one could guide me on a few questions I have:

  1. I have 4 cel files (2 replicates for NORM and Disease resp). I have been able to run siggenes on this dataset where I have 4 labels in the class file groupsnhi.cl op-> (0,0,1,1) and my data has been read into datrmanhi after performing rma. When I run these commands here I receive these errors:

> plot(samnhi.out,seq(0.1,0.6,0.1))
> identify(samnhi.out,ll=FALSE)

warning: no point with 0.25 inches
warning: no point with 0.25 inches
warning: no point with 0.25 inches

Why does this happen.

2) Now I am trying to run EBAM: and when I type I get an error

 > find.out<-find.a0(datrmanhi,groupsnhi.cl,rand=123) Loading required package: affy
Loading required package: affyio
EBAM Analysis for the two class unpaired case.

Warning: There are 1 genes which have variance Zero or no non-missing values.

         The d-value of these genes is set to NA.

        The following object(s) are masked _by_ .GlobalEnv :

         n

        The following object(s) are masked from mat.repeat ( position 5 ) :

         center log.bino n p success x1 x2 x3 x4 x5

Error in optim(rep(0, 6), neglogLik.repeat, method = "BFGS") :

        non-finite finite-difference value [1] In addition: Warning message:
collapsing to unique 'x' values in: approx(Z, Z.norm, z, rule = 2)



I have also tried :
> find.out<-find.a0(exprs2,c(1,1,1,0,0,0),rand=123)
EBAM Analysis for the two class unpaired case.

Warning: There are 1 genes which have variance Zero or no non-missing values.

         The d-value of these genes is set to NA.

        The following object(s) are masked _by_ .GlobalEnv :

         n

        The following object(s) are masked from mat.repeat ( position 3 ) :

         center log.bino n p success x1 x2 x3 x4 x5

        The following object(s) are masked from mat.repeat ( position 6 ) :

         center log.bino n p success x1 x2 x3 x4 x5

Error in optim(rep(0, 6), neglogLik.repeat, method = "BFGS") :

        non-finite finite-difference value [1] In addition: Warning message:
collapsing to unique 'x' values in: approx(Z, Z.norm, z, rule = 2)

I would greatly appreciate any solutions and help to solve this problem.

Thank you,
Appreciate your time.
Regards,
Lolita

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