similar to: Loading Excel file into 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.maimages command. I get this error: Error in

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

Hi Everyone, I have been trying to read some Arrayvision files( 2 channel cDNA) and am having some problem. My code is : setwd('C:/work/data/limma/ndd1'); files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t"); #Normalisation MA=normalizeWithinArrays(RG); #plotPrintTipLoess(MA); #Fit Linear

Hi, there. I used the function read.maimages in limma package to analyze the microarray data .but I got following message >RG <- read.maimages(targets$FileName, source="spot") Error in grep(pattern, x, ignore.case, extended, value, fixed) : invalid argument I don't know what is the matter Thanks a lot Regards Shizhu Zang Department of Biochemsitry Peking

The inst/doc directory of the DAAG package has 6 files coral551.spot, ... that are around 0.85 MB each. It would be useful to be able to zip then, but that as matters stand interferes with the use of the Sweave file that uses them to demonstrate input of expression array data that is in the "spot" format. They do not automatically get unzipped when required. I have checked that

Dear mailing group, I have loaded an Excel file into R by calling it ".csv" and using the "read.csv" function in R. However then I want to use the (limma package specific, I believe) function "hclust", which clusters data in a tree dendrogram, by similarity. However, I receive the errors msg.s: 1) "missing observations in cov/cor" 2) "In

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 conservative (i.e., very

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 does not crash but rather

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 Email: roger.vallejo@ars.usda.gov

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 I do that? Thanks! Max --

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

Hi Hilmar, weird. The memory problem seems be due to recursion (my R, version 3.3.3, says: Error: evaluation nested too deeply: infinite recursion / options(expressions=)?, just write traceback() to see how it happens), but why does it segfault with xlsx? Nb xlsx is the culprit: neither rJava nor xlsxjars cause the problem. On the other hand, quick googling for r+xlsx+segfault returns tons of

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with 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

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 I am trying to use limma, just downloaded it from CRAN. I use R 2.0.1 on Win XP see the following: > library(RODBC) > chan1 <- odbcConnectExcel("D:/Data/mgc/Chips/Chips4.xls") > dd <- sqlFetch(chan1,"Raw") # all data 12000 > # > nzw <-

You asked the same question on the Bioconductor mailing list back in August. At that time, you suggested yourself a solution for how the adjusted p-values should be interpreted. I answered your query and told you that your interpretation was correct. So I'm not sure what more can be said, except that you should read the article Wright (1992), which is cited in the help entry for p.adjust(),

Hello listmemebers, I have data from two-color microarray expression profiling experiments where 3 whole brain (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

Dear list members, I am analysing my microarray data using limma package. Now I encounter several problems. Looking forward to your suggestions! Question 1: During the process of background correction using method="normexp", four warning messages appeared as "NaNs produced in: log(x)" (as you can see in the program posted below). What does that mean? How will it effect the

the following code apprantely, for some grand old reason, induces a syntax error: if (seq[i] = "A") m <- trans[1,] where seq is a vector and trans is a matrix. I cannot for the life of me see why this is wrong. Syntax error is: Error: syntax error in "if (seq[i] =" Sincerely, Norman Goodacre ---------------------------------

I have been trying to open data that I have saved in an excel spread sheet. I saved it as a csv. Then I tried using the read.csv command. However, everytime I do this-- diseasedat<-read.csv("M:/sloan/R/disease/disease.csv", sep=, header = TRUE, fill= TRUE)-- I get an error message: Error in file(file, "r") : unable to open connection In addition: Warning message: