similar to: problems in limma

I would like to load ApoAI.RData. During the operation of reading this data an error occurs. There is also a problem with STF file. > library (limma) > load("ApoAI.RData") Warning message: 'RG' looks like a pre-2.4.0 S4 object: please recreate it > objects() [1] "RG" > names(RG) [1] "R" "G" "Rb"

Hi all, Suppose I have a vector like this: [1] "STAT1" "STAT1" "STAT1" "STAT1" "GAPDH" "GAPDH" "GAPDH" "ACTB" "ACTB" [10] "ACTB" "DDR1" "RFC2" "HSPA6" "PAX8" "GUCA1A" "UBE1L" "THRA" "PTPN21" [19]

Dear experts, I try not to trouble the list again after this question. I want to print this vector into a file > myvec [1] --Control --Control --Control --Control --Control HBA2 HBA1 [8] HBA1 --Control HBB --Control HBB HBA1 MBP [15] --Control HBA1 HBA2 HBB PTGDS GAPDH UBC [22] --Control GAPDH TPT1 HUWE1 PRM1 CKM

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 duplicateCorrelation() is not possible in my case as the spots are not regularly spaced, and I

Dear All, I am analysing a dataset on levels of herbivory in seedlings in an experimental setup in a rainforest. I have seven classes/categories of seedling damage/herbivory that I want to analyse, modelling each separately. There are twenty maternal trees, with eight groups of seedlings around each. Each tree has a TreeID, which I use as the random effect (blocking factor). There are two

Dear R colleagues: Am trying to fit a simple NL model to determine Economical Optimum Nitrogen Rates. The segmented (quadratic + plateau) model only works with some y's, in some cases I get a "singular gradient" error. I'll appreciate any ideas in how to solve the singular gradient error. Thanks, Jose # The following code works using yield2 in the nls model but not using

Hello, I'm attempting to find multiple breakpoints in an association of my response variable (R.AUC) with two explanatory variables ('s.size' and 'bedekking'). The association between 's.size' and 'R.AUC' shows a plateau, but the value when this plateau is reached is differs for different values of 'bedekking'. Initially I thought these different

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This package implements tools for manipulationg digital images and the Propagation Separation approach for smoothing digital images. Version 0.6.1 is a major update with many new features: Input/Output: - - we now keep exif information as comment of an image ~ this information is evaluated to recover the original adimpro-object ~ used to produce

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This package implements tools for manipulationg digital images and the Propagation Separation approach for smoothing digital images. Version 0.6.1 is a major update with many new features: Input/Output: - - we now keep exif information as comment of an image ~ this information is evaluated to recover the original adimpro-object ~ used to produce

Hi there are some predefined self-start functions, like SSmicmen, SSbiexp, SSasymp, SSasympOff, SSasympOrig, SSgompertz, SSflp, SSlogis, SSweibull, Quadratic, Qubic, SSexp (nlrwr) Btw, do you know graphic examples for this functions? The SSexpDecay (exponential decay) for y = (y0 - plateau)*exp(-k*x) + plateau from

Dear All, I would like to make a quadratic with a plateau model in R. Is there a package in R doing this? The bentcableAR package seems won't work. The link below describes what I am looking for in R exactly: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_nlin_sect033.htm -- Thanks so much! Orange help.ly2005@gmail.com [[alternative HTML version

Dear all, I need some help on matrix design and B statistics by using limma package. I want to compare gene expression in 2 groups of cDNA samples. The experiment compares 4 treated mice(#1,#2,#3,#4) and 4 control mice (#5,#6,#7,#8). The target file is FileName Cy3 Cy5 mice1.spot Control_#5 Treat_#1 mice2.spot Treat_#1 Control_#5 mice3.spot Control_#6 Treat_#2

Hello, I have a data set with 9700 records, and 7 parameters. The data were collected for a survey of forest communities. Sample plots (1009) and species (139) are included in this data set. I need to determine how species are accumulated as new plots are considered. Basically, I want to develop a species area curve. I've included the first 20 records from the data set. Point

Dear All, I am doing experiments in live plant tissue using a laser confocal microscope. The method is called "fluorescence recovery after photo-bleaching" (FRAP) and here follows a short summary: 1. Record/ measure fluorescence intensity in a defined, round region of interest (ROI, in this case a small spot) to determine the initial intensity value before the bleaching. This

Dear All, I'm a beginner user in R and I would like to make a quadratic and plateau model in R. Can you help please with an example? Thanks so much -- Ahmed M. Attia Assistant Lecturer El-Khattara farm Station Agronomy Dept., Zgazig Univ., Egypt Visiting Scientist Haskell Agricultural laboratory Agronomy and Horticultural Dept., Univ. of Nebraska-Lincoln ahmedatia at zu.edu.eg

Good evening all, This topic is gone into at a bit more length at my related Stack Overflow question here: http://stackoverflow.com/questions/34647674/why-do-as-methods-remove-vector-names-and-is-there-a-way-around-it There are two lingering issues despite the abundant insight received at SO, namely: 1) _Why_ do as methods remove their arguments' names attribute? This is a fact which is

Dear All! I have a few question about proper syntax for fuzzy rules in sets package (there is only little help about it): 1) how to use negation (NOT) operator there is only OR (||) in example it is NOT, !!, !. I also assume that AND is && 2) where it can be set. For example: area %is NOT% large area %is% NOT large area %is% !large etc... 3) how brackets works (as in typical logical

Hi all, Consider the following function: #### my.func = function(x){ y=ifelse(x>-.5,0,ifelse(x< -.8,abs(x)/2,abs(x))) print(c(x,y)) #print what was tested and what the result is return(y) } curve(my.func,from=-1,1) #### When I attempt to find the maximum of this function, which should be -.8, I find that optimize gets stuck in the plateau area and doesn't bother testing the

This is to announce the release of Icecast 2.4 beta5 (aka 2.3.99.5). We're looking forward to testing and feedback. As this is a beta release please discuss it on the icecast-dev mailing list. (Please do NOT cross-post to both lists, do NOT reply to the icecast mailing list, PLEASE reply to icecast-dev at xiph.org only). * Updated web interface to be fully XHTML compliant and mobile

This is to announce the release of Icecast 2.4 beta5 (aka 2.3.99.5). We're looking forward to testing and feedback. As this is a beta release please discuss it on the icecast-dev mailing list. (Please do NOT cross-post to both lists, do NOT reply to the icecast mailing list, PLEASE reply to icecast-dev at xiph.org only). * Updated web interface to be fully XHTML compliant and mobile