Entering edit mode
>Date: Tue, 6 Mar 2007 11:12:45 +0800 (CST)
>From: zhaodj at ioz.ac.cn
>Subject: [BioC] two questions about limma
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <2959.159.226.67.50.1173150765.squirrel at
mail.ioz.ac.cn>
>Content-Type: text/plain;charset=gb2312
>
>Dear members,
>I encounter two problems when analysing the microarray data employing
the
>package limma. I am using R ver.2.4.1 and limma ver.2.9.13.
>
>
>-------Question 1-------------
>After the backgroundCorrect step, the software gives a series of
warning
>messages as follows:
> > RG.b<-backgroundCorrect(RG,method="normexp",offset=0)
>Corrected array 1
>Corrected array 2
>Corrected array 3
>Corrected array 4
>Corrected array 5
>Corrected array 6
>Corrected array 7
>Corrected array 8
>Corrected array 9
>Corrected array 10
>Corrected array 11
>Corrected array 12
>Corrected array 13
>Corrected array 14
>Corrected array 15
>Corrected array 16
>Corrected array 17
>Corrected array 18
>Warning messages:
>1: Produced NaNs in: log(x)
>2: Produced NaNs in: log(x)
>3: Produced NaNs in: log(x)
>
>I find that some NaNs occur when running the code "out <-
normexp.fit(x)".
>I don't know how to deal with the NaNs.If the NaNs do not influence
the
>selection of the differentially expressed genes, I will ignore them.
If
>not, I seek for your suggestion.
This may be a serious problem, but it's impossible to tell without
seeing your data. Have you checked your data before and after
correction? You need to check whether there are actually any missing
values in the background corrected values. Do the MA plots looks
sensible? Perhaps the problem is caused by exact zeros in your
foreground intensities (which theoretically shouldn't be there).
>-------Question 2-------------
>Another problem is from the duplicateCorrelation. The function
glmgam.fit
>is from the package statmod.
> >corMA.p<-duplicateCorrelation(MA.p,design,ndups=2)
>1: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace)
>2: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace)
>3: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace)
>4: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace)
>
>I don't know the meaning of this warning. Can I ignore them and
proceed to
>the subsequent analysis of the differentially expressed genes? Will
the
>two shortcomings mentioned in the warnings affect the reliability of
the
>differentially expressed genes? If it does,please give some advice.
This is not a problem. See ?duplicateCorrrelation
Best wishes
Gordon
>Thanks to all of you!