similar to: Creating affybatch objects from matrix (data from qPCR array)

Dear all, Is there anyway too generate MA plot for 2 qPCR assays (an array of 2x 400). -- View this message in context: http://r.789695.n4.nabble.com/Bioconductor-MA-plot-for-qPCR-array-tp4182805p4182805.html Sent from the R help mailing list archive at Nabble.com.

I want to use function cbind.na at library(qpcR) I install package qpcR and I can use functions such m1 <- pcrfit(reps, 1, 2, l5) > AICc(m1) [1] -102.5843 but when i try cbind.na(1, 1:7) i take message Error: could not find function "cbind.na" Thanks -- View this message in context: http://r.789695.n4.nabble.com/library-qpcR-cbind-na-tp4023339p4023339.html Sent from the

I am using R on a Windows XP professional platform. The following code is part of a bigger one CODE press=function(y,x){ library(qpcR) models.press=numeric(0) cat("\n") dep=y print(dep) indep=log(x) print(indep) yfit=dep-PRESS(lm(dep~indep))[[2]] cat("\n yfit\n") print(yfit) yfit.orig=yfit presid=y-yfit.orig press=sum(presid^2)

Hello, Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array) Im useing this script: library(matchprobes) library(affy) library(AnnotationDbi) library(hgu133plus2probe) library(hgu133aprobe) library(hgu133a.db) u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch u133a1 = ReadAffy() # reading hgu133a cel file into affybatch u133a2 = ReadAffy() # reading hgu133a

Hi All, I have microarray data that does not come in a CEL file. Currently it is in the form of columns = individual samples and rows = individual probes. There are about 79 columns and it is in a tab delimited text file. Is there a way to convert this file into an AffyBatch so that I can run expresso with it? Thanks, George

promptClass fails to identify methods associated with the class. Here is a fix: Index: promptClass.R =================================================================== --- promptClass.R (revision 41719) +++ promptClass.R (working copy) @@ -165,7 +165,7 @@ if (nmeths > 0) { .meths.body <- " \\describe{" for (i in 1:nmeths) { - .sigmat

Inline. -- Bert On Tue, Apr 26, 2016 at 2:25 PM, Andr? Luis Neves <andrluis at ualberta.ca> wrote: > Ok. I`m trying to run a Poisson glmm with an observation-level random > intercept. But I`m getting the following error for the 'Baci' variable: > > 'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in > pwrssUpdate'. I guess this message

Ok. I`m trying to run a Poisson glmm with an observation-level random intercept. But I`m getting the following error for the 'Baci' variable: 'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in pwrssUpdate'. I guess this message is because the baci variable is not a an integer, and cannot be transformed into an integer as R has a threshold of 2x10^9 even in

Running R2.4.0 on Apple Mac OS X 10.4.8, in Emacs ESS mode, and also R.app. In an attempt to learn a bit more about a particular method (geneNames in package affy) I invoked getMethods("geneNames") which produced geneNames methods, but not the one in affy (output below). I had to know the signature (AffyBatch) in order to find the method > getMethod("geneNames",

dear all, I have a problem with a masked object in a package we created here. we make a package for a workflow of internal analysis of microarray data. to create the package we used: > install.packages(pkgs="affyAnalysis", repos=NULL) > R CMD INSTALL affyAnalysis Erzeuge Verzeichnisse ... Erzeuge DESCRIPTION ... Erzeuge NAMESPACE ... Erzeuge Read-and-delete-me ... Kopiere

Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R

Hi, I have two data set of normalized Affymetrix CEL files, wild type vs Control type.(each set have further three replicates). > wild.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= > Dicer.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617

I am using LOF.test() function from the qpcR package and got the following result: > LOF.test(nlregmod3) $pF [1] 0.97686 $pLR [1] 0.77025 Can I conclude from the LOF.test() results that my nonlinear regression model is significant/statistically significant? Where my nonlinear model was fitted as follows: nlregmod3 <- nlsr(formula=y ~ theta1 - theta2*exp(-theta3*x), data =

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of

Hi, Many apologies for sending this twice. I accidentally hit the send button before I finished writing my mail. I am new to R and I hope someone can help me with my problem. I am trying to draw a side by side barplot. There is a main experiment and there are many sub experiments within the main experiment. I would like to draw a bar plot showing the number and type of sub_experiments done for

Hej, Calling newuoa (from the minqa package) makes R crash when the package rgl is loaded first. This however only on certain selected data. The data used for testing (saved to 'bugs.R'): xvals = c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36) yvals =

Hi, I am looking to build even quintiles for a set of data. I managed to get it done, but I would like to know if there is a more direct way to write the data from my loop output x in the bottom of the code into the "empty" matrix p1, which I filled with NA''s. The way I am doing it at the moment is, more or less adding the matrix x after p1 and then deleting in a second step

> On Apr 10, 2016, at 9:38 AM, David Winsemius <dwinsemius at comcast.net> wrote: > >> >> On Apr 10, 2016, at 3:11 AM, Murray Efford <murray.efford at otago.ac.nz> wrote: >> >> Martin - >> Thanks, but although hatvalues() is useful for calculating PRESS, I can't find anything directly relevant to my question in the influence help pages. After

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

Hi I'm running the latest R on a presumably up to date Linux server. 'Doing something silly I'm sure, but can't see why my saved PLMset objects come out all wrong. To use an example: Setting up an example PLMset (I have the same problem no matter what example I use) > library(affyPLM) > data(Dilution) # affybatch object > Dilution = updateObject(Dilution)