Displaying 20 results from an estimated 64 matches for "assays".
Did you mean:
assay
2003 Nov 10
8
Memory issues..
Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My
sample size is about 2965 and 3 factors:
year (5 levels), ssize (4 levels), condition (2 levels).
When I issue the following command:
>
lme(var~year*ssize*condition,random=~ssize+condition|subject,data=smp,method
="ML")
I got the following error:
Error in logLik.lmeStructInt(lmeSt, lmePars) :
2020 Sep 24
1
How to use `[` without evaluating the arguments.
...#' limitations of the `[` S4 method.
#'
setOldClass('long.table')
#' LongTable class definition
#'
#' Define a private constructor method to be used to build a `LongTable` object.
#'
#' @param drugs [`data.table`]
#' @param cells [`data.table`]
#' @param assays [`list`]
#' @param metadata [`list`]
#'
#'
#' @return [`LongTable`] object containing the assay data from a
#'
#' @import data.table
#' @keywords internal
.LongTable <- setClass("LongTable",
slots=list(rowData='data.table',...
2012 Apr 10
3
How to get the SS and MS from oneway.test?
Hello everyone:
I'm a new member of this group.
I have a question about "oneway.test".
When I use "anova(lm(....))" to analysis the
ANOVA,
I can get the information about Sum Sq and Mean
Sq.
(The R code and the results are as follows.)
2010 Apr 29
1
How to estimate the residual SD for each sample separately in mixed-effects model?
Dear R-helpers,
I am developing a Mixed-Effects model for a study of immunoassays using
'lme4' library. The study design is as follows: 10 samples were run
using 7 different immunoassays, 3 times each, in duplicates. Data
attached. I have developed the following model:
c.lme <- lmer(Result~SPL + (SPL|Assay/Run) -1, data=data)
This model has excellent predictions...
2006 Feb 07
0
lme and Assay data: Test for block effect when block is systematic - anova/summary goes wrong
Consider the Assay data where block, sample within block and dilut within block is random.
This model can be fitted with (where I define Assay2 to get an ordinary data frame rather
than a grouped data object):
Assay2 <- as.data.frame(Assay)
fm2<-lme(logDens~sample*dilut, data=Assay2,
random=list(Block = pdBlocked(list(pdIdent(~1), pdIdent(~sample-1),pdIdent(~dilut-1))) ))
Now, block
2006 Jun 21
1
eliminating a do loop
Using a "by() statement, I am preparing ANOVA's for multiple experiments,
and using simint() to generate confidence intervals.
This works fine.
simint.by.fit <- by(analytes.dfr, list(Assay = analytes.dfr$analyte ),
function(data) (simint(value ~ tx, data = data,type='Tukey' ) ) )
I can separately prepare plots of the confidence intervals, and I can
prepare separate plots
2009 Nov 05
0
analysing HTS assay plates for spatial effects
Hi, I'm have some data on a grid (specifically high throughput assay plates)
and am interested in evaluating measures of spatial autocorrelation to flag
plates for corrections. I have been using moran.test and geary.test from the
spdep package.
My approach is as follows:
## plate is a matrix of data
coords <- expand.grid(1:32, 1:48)
x <- as.numeric(plate)
moran.test(x,
2008 Dec 07
2
concordance correlation coefficient using R
Hi.
I have data which i would want to assess the degree of agreement
between two assays, e.g., to evaluate reproducibility or for
inter-rater reliability. I have used the Pearson product-moment
correlation coefficient. It looks good ranginging between 0.90 to
0.998. Though this looks good. I am told the Concordance correlation
coefficient will give a better picture of how reproducibl...
2012 Jun 14
1
Can someone recommend a package for SNP cluster analysis of Fluidigm microarrays?
...commodate a negative control sample by not
including it in any genotype cluster.
I'm looking at both nuclear and mitochondrial DNA so hopefully it can be
sophisticated enough to set the number of cluster between two or three
within the array.
These genotyping arrays are either 48 samples x 48 assays, 96x96, or 192x24
and it would be nice if it could accommodate any range of samples and
assays.
the data headings from the csv are:
ID,Assay,Allele Y,Allele X,Name,Type,Auto,Confidence,Final,Converted,Allele
Y,Allele X
where Allele Y and Allele X are the plotted values and the vectors within
the...
2012 Jan 22
1
How to construct a formula
Hi,
I need to construct a formula programaticly, and pass it to a function
such as the linear mixed model lme. The help says it requires "a
two-sided linear formula object describing the fixed-effects part of the
model" but I do not know how to create this formula. I have tried
various things using formula(x, ...), as.formula(object, env =
parent.frame()) and as.Formula(x, ...)
2010 Dec 13
1
Multivariate binary response analysis
...lasses of chemicals (a MANOVA-type analysis). Interest is focused on where response(s) are occurring, any associations among responses, and ultimately on possible biological mechanisms (the fish are tested for behavioral activity prior to this assay, and then ground up to provide RNA for microarray assays. A-lotta-data!).
What I *wish* I could do is something like glm(response.matrix ~ treat/vial, family=binomial(logit), data=zf.dat) but I know this can't be done. I came across the baymvb (Bayesian analysis of multivariate binary data) package in the R contributed packages archives, but it is n...
2003 May 12
1
update.lme trouble (PR#2985)
Try this
data(Assay)
as1 <- lme(logDens~sample*dilut, data=Assay,
random=pdBlocked(list(
pdIdent(~1),
pdIdent(~sample-1),
pdIdent(~dilut-1))))
update(as1,random=pdCompSymm(~sample-1))
update(as1,random=pdCompSymm(~sample-1))
update(as1,random=pdCompSymm(~sample-1))
update(as1,random=pdCompSymm(~sample-1))
I'm
2007 Jun 26
4
Can I stub a method on a belongs_to association:
describe Asset, " when destroyed" do
fixtures :assets, :videos, :sites, :publish_settings
before(:each) do
@asset = assets(:test_asset)
@mock_hook = mock("hook")
@asset.video.stub!(:hook).and_return @mock_hook # error occurs here
end
it "should call the delete hook" do
@mock_hook.should_receive(:update).with("test_video",
2010 Oct 13
5
Regular expression to find value between brackets
Hi,
this should be an easy one, but I can't figure it out.
I have a vector of tests, with their units between brackets (if they have
units).
eg tests <- c("pH", "Assay (%)", "Impurity A(%)", "content (mg/ml)")
Now I would like to hava a function where I use a test as input, and which
returns the units
like:
f <- function (x) sub("\\)",
2010 Mar 09
3
Help with ANOVA in R
Hi
I am attempting Anova analysis to compare results from four groups
(Samp1-4) which are lists of intensities from the experiment. I am
doing this by first creating a structured list of the data and then
conducting the ANOVA (Script provided below). Im an R beginner so am
not sure if I am using this correctly. Two major questions I have are:
1)
Is using the code (zzz.aov <- aov(Intensity ~
2013 Sep 11
0
Nonclinical Statistician
Pfizer is hiring a statistician supporting early drug discovery for Global
Medicinal Chemistry and Pharmacokinetics, Dynamics and Metabolism (PDM).
If interested, go to http://pfizercareers.com/ and search for job ID
985944. The location is Groton, Connecticut.
Responsibilities
The statistician will have a consulting-type role supporting a large pool
of scientists in two large platform line
2017 Aug 08
1
Bug?
Hello,
In my code I found something that looks like an anomaly, I found a reproducible example in which I am just trying to compare each row in a data frame against the first row:
a<-data.frame(row=c("B","C","B"),column=c(2,2,10),assay=c("Assay1","Assay1","Assay1"),plate=c(1,1,1),stringsAsFactors=FALSE)
apply(a[1:2,],1,function(x) {
2012 May 23
3
applying cbind (or any function) across all components in a list
#If I have two lists as follows
a1<- array(1:6, dim=c(2,3))
a2<- array(7:12, dim=c(2,3))
l1<- list(a1,a2)
a3<- array(1:4, dim=c(2,2))
a4<- array(5:8, dim=c(2,2))
l2<- list(a3,a4)
#how can I create a new list with the mean across all arrays within the
list, so all components are included? As an example for [[1]];
cbind((l1[[1]][,1]+l2[[1]][,1])/2,
2011 Nov 21
0
Programmer position in the Gottardo lab at the Fred Hutchinson Cancer Research Center
...ummary:
The successful applicant will integrate a dynamic team of biostatisticians, bioinformaticians, computer scientists, and programmers lead by Dr. Raphael Gottardo to support the development of software packages to analyze and integrate high throughput data from next generation immunological assays (e.g. Fluidigm, CyTOF, next generation sequencing). The position will involve the development of efficient packages for the analysis of high-throughput data, including computational algorithms development and implementation of creative solutions for large volume data management and processing. The...
2008 Oct 29
1
Regression versus functional/structural relationship?
Hi,
I am dealing with the following problem. There are two biochemical assays,
say A and B, available for analyzing blood samples. Half the samples have
been analyzed with A. Now, for some insurmountable logistic reasons, we
have to use B to analyze the remaining samples. However, we can do a
comparative study on a small number of samples where we can obtain
concentration...