Displaying 20 results from an estimated 3000 matches similar to: "RMA question"
2009 Dec 26
1
[BioC] How to do RMA without summary to probeset level?
I think that you misunderstood me.
As far as I know, RMA does three things: background correction,
quantile normalization, and summary from probes to probesets. I want
the probe values after background correction and quantile
normalization but before the summary.
On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> pm(data)
>
> b
>
> On Dec
2007 Dec 24
3
Affy Package
Dear R Users,
In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best:
bgcorrect.metod = rma rma2 mas
normalize.method = qspline quantiles loess
pmcorrect.method = pmonly subtractmm mas
summary.method = liwong avgdiff medianpolish mas
There are many options within each method. I would appreciate a hint on the best
2007 Aug 06
1
Problems with expresso
Hello,
I want to use expresso for preprocessing the hgu133a-spikein data from
affycompII. But there is an error:
> library(affy)
> path <- "z:/Microarray/hgu133a-spikein/rawdata"
> celFile <- list.celfiles(path=path,full.names=TRUE);
> affyBatch <- ReadAffy(filenames=celFile[1:6]);
> eset1 <-
2011 Sep 08
1
predict.rma (metafor package)
Hi
(R 2.13.1, OSX 10.6.8)
I am trying to use predict.rma with continuous and categorical variables. The argument newmods in predict.rma seems to handle coviariates, but appears to falter on factors. While I realise that the coefficients for factors provide the answers, the goal is to eventually use predict.rma with ANCOVA type model with an interaction.
Here is a self contained example
2009 Jul 20
1
package lmodel2: p-value RMA fitting?
Hi *,
is there a way to obtain some kind of p-value for a model fitted with RMA
using the lmodel2 package?
I know that p-values are discussed and criticized a lot and as you can image
from my question I'm not
very much of a statistican (only writing my bachelor thesis).
As fare as I understood the confidence interval statistic correctly, a
coefficient is regarded as statistically
significant
2009 Dec 04
1
z to r transformation within print.rma.uni and forest from the package metafor
Dear R community,
I'm using the ,metafor'-package by Wolfgang Viechtbauer (Version: 0.5-5) to
calculate random-effects meta-analyses using Correlations and Sample Sizes
as the raw data.
(By the way: Really a nice piece of work, Wolfgang! Thanks heaps.)
I specified the "rma.uni' function so that it looks like this:
MAergebnis<-rma.uni(ri=PosOutc, ni=N,
2011 Jul 18
1
Extract confidence intervals from rma object (metafor package)
Dear R-experts!
I am working on some meta-analysis using the metafor package. I would like
to extract values of the confidence intervals of the effect sizes of the
single studies from an rma object. Those values are printed out when
plotting a forest plot using the forest function on the rma object, however
I was not able to locate them.
Many thanks for your help!
Jokel
[[alternative HTML
2012 Jul 24
1
Annotate forest plot 'forest.rma()' for meta-analysis with metafor package
Dear R-experts,
The forest.rma() function from the metafor package creates nice forest
plots for presenting the results of a meta-analysis. These plots can be
annotated for e.g. giving names to the columns. E.g. as in the
documentation of the package:
data(dat.bcg)
### meta-analysis of the log relative risks using a random-effects model
res <- rma(ai=tpos, bi=tneg, ci=cpos, di=cneg,
2006 Mar 03
3
Sipura RMA
Anyone have any luck RMAing a Sipura phone since the Cisco take over?
Sipura only has support via email or fax to end users and I haven't
gotten a response to either for over 2 months.
Linksys Support will jump you through all their scripted hoops to
resolve your problem (they hope if they speak with a thick enough accent
and make repeat the same steps over and over again that you will just
2011 Oct 16
0
background normalization in rma() in the affy package
Hi,
i was looking into the documentation for the rma() function in affy()
package, and was trying to figure out how exactly the background
normalization is done. I read all three papers cited in the rma()
documentation, but the most detailed explanation i could find was in Irizary
et al., 2003, where they state that they compute
B(PM_{ijn}) = E[s_{ijn} | PM_{ijn}]
where s_{ijn} is assumed to
2006 Jul 11
1
test regression against given slope for reduced major axis regression (RMA)
Hi,
for testing if the slope of experimental data differs from a
given slope I'm using the function
"test_regression_against_slope" (see below).
I am now confronted with the problem that I have data which
requires a modelII regression (also called reduced major axes
regression (RMA) or geometric mean regression). For this I use
the function "modelII" (see below).
What
2004 May 14
2
rma and gcrma do not work in R 1.9.0
I run R 1.9.0 on windows 2000, and have the following libraries installed:
affydata_1.3.1
affy_1.4.23
Biobase_1.4.10
DynDoc_1.3.14
gcrma_1.0.6
hgu133acdf_1.4.3
hgu95av2cdf_1.4.3
hgu95av2probe_1.0
matchprobes_1.0.7
moe430acdf_1.4.3
multcomp_0.4-6
mvtnorm_0.6-6
rae230acdf_1.4.3
reposTools_1.3.29
rgu34acdf_1.4.3
tkWidgets_1.5.1
widgetTools_1.2.7
1. The rma function (in affy library) always crashes.
2007 Aug 03
4
FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
Hi all,
What are current methods people use in R to identify
mis-spelled column names when selecting columns
from a data frame?
Alice Johnson recently tackled this issue
(see [BioC] posting below).
Due to a mis-spelled column name ("FileName"
instead of "Filename") which produced no warning,
Alice spent a fair amount of time tracking down
this bug. With my fumbling fingers
2011 May 28
7
Have my RMA... Now what??
I have a raidz2 pool with one disk that seems to be going bad, several errors are noted in iostat. I have an RMA for the drive, however - no I am wondering how I proceed. I need to send the drive in and then they will send me one back. If I had the drive on hand, I could do a zpool replace.
Do I do a zpool offline? zpool detach?
Once I get the drive back and put it in the same drive bay..
2009 Jan 27
1
Problem with RMA using limma, oligo and pdInfoBuilder packages
Hi,
I am a Ph.D. student from Québec, Canada. I’m a beginner with R and
Bioconductor. Until now the only experience I have is in analyzing
microarray data using affy and limma packages. Now I am trying to analyze
Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth
moderated t test on those arrays. Since no cdf official package is available
for those arrays, after reading many
2009 Sep 17
1
boxplot
Hi,
I m not able to plot normalized data(normalization by rma) using boxplot. I
don't know why?
basically, object(formed of normalized data) belong to ExpressionSet class.
It is showing error
Error in x[!xna] : object of type 'S4' is not subsettable
In addition: Warning messages:
1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(x) : is.na()
2011 Jun 13
2
cause 'memory not mapped'
Dear R-help
Hi,
I'm Won.
I try to do microarray normalization by R.
I use justRMA function within affy package, got error about segment fault.
I don't know why it happen.
I attached error below.
Please help me.
Thank you.
Cheers,
Won
=======================
OS : Redhat linux
Cpu : intel xeon X5570
Memory : 26Gb
&
OS : Ubuntu
Cpu : intel q6600
Memory : 8Gb
2011 Mar 29
0
Plotting 95% Confidence Intervals around RMA slope
Hi,
I'm regressing various body dimensions upon body mass using the 'lmodel2' function, as I'm keen to obtain both OLS and RMA slope values. I also wish to create a plot of the regressions, with the 95% confidence interval of both the slope and intercept. I know how to plot 95% ci bands of the OLS slope using lm with the 'predict' function and 'matlines'. Does
2002 Sep 20
0
Linksys EFG20, RMA XH01210298
Forwarded to: ismtp[samba@samba.org]
cc:
Comments by: Charles J. Huenke@Admin@SAC
Comments:
Please offer any input you may have on the issue described below.
Thank you.
Chuck Huenke
Delaware Statistical Analysis Center
(302) 739-3680
-------------------------- [Original Message] -------------------------
We received a replacement EFG20 on the referenced
2008 Aug 18
1
exonmap question: rma (or justplier) crashes
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