search for: limma

Dear Sirs, How can I revert to an older limma version? Typing "install.packages("limma")" in R gives a list of mirrors. How can I install the version I want after I obtain and untar the file (e.g, limma_2.9.1.tar.gz)? I am running R 2.5.0 on a Linux machine (CentOS 5). When using limma it will not go past the read.maimage...

Hi, this is a problem that occurs in the presence of two libraries (limma, xlsx) and leads to a crash of R. The problematic code is the wrong application of sweep or the product ("*") function on an LIMMA MAList object. To my knowledge, limma does not define a "*" method for MAList objects. If only LIMMA is loaded but not package xlsx, the code d...

Hi, following up on my own question, I found smaller example that does not require LIMMA: setClass("FOOCLASS", representation("list") ) ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > ma * ma$M Error: C stack usage 7970512 is too close to the limit > library(xlsx) Loading required package: rJava Loading required package: xls...

Dear All, How to cite the PDF user's guide for the LIMMA package? This is not about how to cite the LIMMA package. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture, ARS National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Ema...

Hi, I am following the protocol outlined here for analysis of single channel Agilent microarray data: http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma I keep getting the following error message when using Limma's read.maimages function to load my data into an RGList object: Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of items to replace is not a multiple of replacement length I think this may be due to my Agilent raw data t...

...-specific. It would be interesting to see whether anyone with a Mac can reproduce it. kind regards, j. On 19 April 2017 at 10:01, Hilmar Berger <berger at mpiib-berlin.mpg.de> wrote: > Hi, > > following up on my own question, I found smaller example that does not > require LIMMA: > > setClass("FOOCLASS", > representation("list") > ) > ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > > > ma * ma$M > Error: C stack usage 7970512 is too close to the limit > > > library(xlsx) > Loading requ...

Dear mailing group, This is my first time here. Glad to have this resource! I am currently trying to load an Excel file into R (limma package loaded) using the source(*name of directory*) command, but it cannot open the file. I renamed the file as .R and .RData, to no avail. The Excel data contains one gene name per row and about 100 data points per gene (columns). I am only used to loading preprepared microarray data with...

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite cons...

...() R Under development (unstable) (2017-04-18 r72542) Platform: x86_64-apple-darwin16.5.0 (64-bit) Running under: macOS Sierra 10.12.4 Best wishes Wolfgang 19.4.17 10:01, Hilmar Berger scripsit: > Hi, > > following up on my own question, I found smaller example that does not > require LIMMA: > > setClass("FOOCLASS", > representation("list") > ) > ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > >> ma * ma$M > Error: C stack usage 7970512 is too close to the limit > >> library(xlsx) > Loading requir...

Hi all. I've got a really dumb question for anyone. How do I write the output of a limma analysis (basically the topTable) to a text file? I want to output the topTable for the entire microarray (not really a topTable anymore I suppose..). Thanks for any advice! -Josh

I have a very basic question about limma. Assume I have experiments from 3 or more RNA sources in a reference design. It is easy to define individual contrasts but I want to specify a contrast matrix that tests for significant differences among ALL the different RNA sources (i.e. the analogous thing to a simple One-Way ANOVA). How can...

Dear R help, In limma package, contrasts.fit() function is very useful. I am wondering whether there is a similar function for lme object, which means given a mixed linear model fit, compute estimated coefficients and standard errors for a given set of contrasts. Thanks, Shirley

...> > j. > > > > > > On 19 April 2017 at 10:01, Hilmar Berger <berger at mpiib-berlin.mpg.de > <mailto:berger at mpiib-berlin.mpg.de>> wrote: > > Hi, > > following up on my own question, I found smaller example that does > not require LIMMA: > > setClass("FOOCLASS", > representation("list") > ) > ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > > > ma * ma$M > Error: C stack usage 7970512 is too close to the limit > > > lib...

...data in R. I used the following code to draw a loess fit and got the output as >?lines(lowess(log(abs(t(res))), log(abs(t(synthesised)))), col="red") Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf in foreign function call (arg 1) Then I thought to use your Limma package for background correction. Do you think it's a right choice ? However, I installed Limma using > source("http://www.bioconductor.org/biocLite.R") > biocLite("limma") > biocLite("statmod") > library(limma) and then used the commands which gene...

...ed, December 22, 2004 12:11 am, r.ghezzo at staff.mcgill.ca said: > ----- Forwarded message from r.ghezzo at staff.mcgill.ca ----- > Date: Mon, 20 Dec 2004 15:45:11 -0500 > From: r.ghezzo at staff.mcgill.ca > Reply-To: r.ghezzo at staff.mcgill.ca > Subject: [R] problems with limma > To: r-help at stat.math.ethz.ch > > I try to send this message To Gordon Smyth at smyth at vehi,edu.au but it bounced > back, so here it is to r-help Questions about limma should be sent to the Bioconductor mailing list (the address is given in the introduction of the Limma Use...

...th significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have different probesets with differential transcriptional outcomes. I did this based on the affy and limma manuals like: targets file: Name FileName Target 0h1 GSM286031.CEL control 0h2 GSM286032.CEL control 0h3 GSM286033.CEL control 3h1 GSM286034.CEL three 3h2 GSM286035.CEL three 3h3 GSM286036.CEL three 6h1 GSM286037.CEL six 6h2 GSM286038.CEL six 6h3 GSM286039.CEL six library(affy) library(limma) li...

Hi, I have a question about limma. I have data from spotted arrays. I have class A and Class B on the same slide. In Limma if I put class A as the reference (ref), are the list of genes I get in the output for class A or class B? #design <- modelMatrix(targets, ref="classA") design Josephine Brennan [[alternat...

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <- cbind(...

Hello Limma users A quick question, I hope: I have dual-channel spotted expression arrays in a simple loop design (no dye swaps), viz: 1 vs reference 2 vs 1 3 vs 2 reference vs 3 There are 4 replicate spots for each probe on each array. It seems as if getting meaningful spot summary results using duplic...

...ain (WB) samples were compared to 3 Mauthner Cells (MC) in a loop design (-> MC #1 -> WB #1 -> MC #2 -> WB #2 -> MC #3 -> WB #3 -> MC #1 ->). In addition to phenotype analysis I would also like to run an individual analysis making all pair-wise comparisons. I'm using the LIMMA package in R to do this. The problem is that the contrast matrix that you have to set up requires that one of the samples be designated as a reference, but in doing so you lose the sample. My question is this, is it possible to run individual analysis with this data set without losing one as a refe...