1 Oct 2004 01:06
1 Oct 2004 07:47
marrayLayout difficulties
Hi, all - I'm experiencing very poor performance using the marray package (20 minutes to normalize a single <32,000 spot microarray). Can someone tell me whether this is normal, or what I'm doing wrong? In the process of hunting down some errors, I also noticed some odd (to me) behavior in the marrayLayout maSub slot assignment method, described below. An attempt to "correct" this results in a much faster normalization (~1 minute), which looks good according to the MA plot but produces different numbers in maM than the slower calculation. It seems unlikely that either result is correct (I can choose between suspiciously bad performance, or messing with the marrayLayout object's internals). Thanks for any suggestions - details follow. I'm using R version 1.9.0 on a sparc system running Solaris 2.9. My marray version is 1.5.14. I have a text file, "dat.txt," containing the data I want to normalize. 10 columns, all numeric: in order, FEATURE spot number 1 - 31736 SECTOR unnecessary and unused ROW " COL " PLATE ID of printing plate Gf green channel foreground Rf red channel foreground(Continue reading)
1 Oct 2004 09:52
Re: marrayLayout difficulties
Hi Jeremy, That sounds very slow from my experience. Which image analysis software did you get your data from? If you send me an example file off-line, I will take a look at it for you, I need to take a look to see if maSub was set properly, as this does make a big different in print-tip normalization. Alternatively, try the latest verion 1.5.17 that is temporary place at http://arrays.ucsf.edu/software/ maNorm was previously very slow for global lowess normalization for larget number of spots but in the new version, we have speed up the code with sampling. However, I don't think this was your problem. I will also suggest trying the swirl data within the marray package and see how long that take on yoru computer data(swirl) norm <- maNorm(swirl) If that takes a min or so that there is something wrong with your data setup. Cheers Jean On Thu, 30 Sep 2004, Jeremy Gollub wrote:(Continue reading)
1 Oct 2004 13:35
Extracting Single Channel Intensities in limma
Hi I have performed print-tip loess normalisation followed by quantile normalisation in limma. I have then converted the resulting MAList object back to an RGList object using RG.MA(). I now want to extract the single channel intensities from this normalised RGList object to create *new* RGList objects which represent comparisons between samples that were not made on the arrays directly. However, as RG.MA gives me log2(intensity) back rather than raw intensity, I presume I need to un-log this data before sending it down my normal analysis pipeline of RGList -> MAList -> lmFit(MAList) -> eBayes() -> topTable() ?? Thanks Mick
1 Oct 2004 13:52
Re: Extracting Single Channel Intensities in limma
Mick, Is there no way to do this with an appropriate contrast matrix? That seems a safer/more appropriate way of using your two-channel data. Sean On Oct 1, 2004, at 7:35 AM, michael watson (IAH-C) wrote: > Hi > > I have performed print-tip loess normalisation followed by quantile > normalisation in limma. I have then converted the resulting MAList > object back to an RGList object using RG.MA(). I now want to extract > the single channel intensities from this normalised RGList object to > create *new* RGList objects which represent comparisons between samples > that were not made on the arrays directly. > > However, as RG.MA gives me log2(intensity) back rather than raw > intensity, I presume I need to un-log this data before sending it down > my normal analysis pipeline of RGList -> MAList -> lmFit(MAList) -> > eBayes() -> topTable() ?? > > Thanks > Mick > > _______________________________________________ > Bioconductor mailing list > Bioconductor@... > https://stat.ethz.ch/mailman/listinfo/bioconductor(Continue reading)
1 Oct 2004 14:06
Re: Rgraphviz install issues
Jeff - thanks for the advice, but unfortunately, no dice.... I download
the development Rgraphviz pacakge, and using the same routine with
exporting my library location for graphviz, get the same error.... any
more ideas? the offending line seems to be this: ld: can't locate file
for: -ldotneato
cheers
andrew
dyn092203:~ apb$ export LD_LIBRARY_PATH=/opt/local/lib/graphviz
dyn092203:~ apb$ sudo R CMD INSTALL /Users/apb/Rgraphviz_1-1.4.23.tar.gz
Password:
* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for dotneato-config...
/opt/local/bin//dotneato-config
/opt/local/bin//dotneato-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/opt/local/include/graphviz -I/usr/local/include -Wall -fno-common
-g -O2 -c Rgraphviz.c -o Rgraphviz.o
In file included from /opt/local/include/graphviz/render.h:45,
from common.h:22,
from Rgraphviz.c:1:
/opt/local/include/graphviz/macros.h:34:1: warning: "NEW" redefined
In file included from common.h:13,
from Rgraphviz.c:1:
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1:
warning: this is the location of the previous definition
(Continue reading)
1 Oct 2004 15:07
Re: Extracting Single Channel Intensities in limma
On Oct 1, 2004, at 8:50 AM, michael watson (IAH-C) wrote: > You tell me, contrast matrices are a black art when it comes to > complicated experiments. > > What I have are two conditions, +ve and -ve, and a control. The design > of the experiment is rather odd. I have arrays that are: > > -ve / +ve > -ve / +ve > -ve / +ve > Etc > Etc > -ve / Control > > What I want are: > > -ve / Control > -ve / Control > Etc > +ve / Control > +ve / Control > Etc > > I figured that by using the methods decsribe in limma, I could subtract > the single channel intensity data, and completely re-arrange the > experiment such that all of my -ve and +ve values have the control as > the denominator. >(Continue reading)
1 Oct 2004 15:22
RE: Extracting Single Channel Intensities in limma
I'm not sure I told you enough about the experimental design to get this right, so if we want to explore this using contrast matrices, I better add the little detail that might make things more complicated. Although I can assume all my negative samples are replicates of the same thing, I can't assume that all my positive samples are. It's a *very* strange experiment, but I have 8 +ve phenotype samples and they are NOT replicates of one another. So I actually have a factor with nine levels (the 8 +ve phenotypes and the control) all against a common reference, which is the -ve phenotype. To complicate things further, sometimes the -ve is labelled Cy5, sometimes Cy3, and only two of the +ve phenotypes have replication, in the form of a single dye-flip. This is why I really wanted to extract the single channels and then construct "dummy" microarray experiments(Continue reading)-----Original Message----- From: Sean Davis [mailto:sdavis2@...] Sent: 01 October 2004 14:08 To: michael watson (IAH-C) Cc: Bioconductor Subject: Re: [BioC] Extracting Single Channel Intensities in limma On Oct 1, 2004, at 8:50 AM, michael watson (IAH-C) wrote: > You tell me, contrast matrices are a black art when it comes to > complicated experiments. > > What I have are two conditions, +ve and -ve, and a control. The > design of the experiment is rather odd. I have arrays that are:
1 Oct 2004 15:38
Limma p-value distributions, false +ve/-ve etc...
Hi, I guess the simple question is would you expect or have you seen a 'standard' distribution of p-values for a treated-untreated comparison (3 reps) after the eBayes procedure in Limma? Expressed in my usual 'comprehensive' style(Continue reading)
1 Oct 2004 16:29
Re: Rgraphviz install issues
> Jeff - thanks for the advice, but unfortunately, no dice.... I download > the development Rgraphviz pacakge, and using the same routine with > exporting my library location for graphviz, get the same error.... any > more ideas? the offending line seems to be this: ld: can't locate file > for: -ldotneato That doesn't appear to be the same error at all, unless I'm missing something. That error means that you haven't pointed your LD_LIBRARY_PATH to where the graphviz libraries are sitting.
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