similar to: error while opening vignette DESeq2

There are two line 216 and 218 Three development stages 5 WEEK (5W), 7W, 9W. Three tissue: Ca, Co, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData and design formula. library("DESeq2")

Hi... I have a dataframe with n columns and n rows. I need to find how many rows contains zero raw read count across all column. Thanks -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [[alternative HTML version deleted]]

Dear All, I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames)

Dear expeRts, I would simplify following code. --------------------------------------------- youtput <- function(x1, x2){ n <- length(x1) y <- vector(mode="numeric", length=n) for(i in 1:n){ if(x1[i] >=5 & x1[i] <= 10 & x2[i] >=5 & x2[i] <=10) y[i] <- 0.631 * x1[i]^0.55 * x2[i]^0.65 if(x1[i] >=10 & x1[i] <= 15 &

I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) >

Howdy, R Grues I have enjoyed R, but I cannot solve one problem easily. Please help my problem. When I tried the R script, I got the following Error. This error results from input data file exported through a Excel spreadsheet software. Error in step(lm(pop.rate ~ as.numeric(year) + as.factor(policy) + as.numeric(nation.grant) + ?: ??number of rows in use has changed: remove missing values?

Hello, My name is Chung Hae Young, and I work for NCsoft in Seoul, Korea. I am currently working on a online game development project. I have some questions regarding Ogg Vorbis. I want to change the library source and change Ogg game music files so the file can only be played within the game. I want to know if I can modify the library. And if I modify it, will if cause any legal

Dear All, I am learning R so it's a very simple problem but I do not understand while I am not able to generate a graph from two vectors. when I type this code, it generates a very nice graph. pdf("mygraph.pdf") > attach(mtcars) > plot(wt,mpg) > abline(lm(mpg~wt)) > title("Regreesion of mpg") > detach(mtcars) > dev.off() But I am trying to create a

Hi all , I'm running Debian Etch . I just finished configuring SAMBA as PDC to authenticate against LDAP server which works. The system in question uses default debian etch packages. As My Linix/unix accounts can authenticate against it. The LDAP works. I Used the default shipped smbldap-populate script to setup SAMBA. Everything seems to work as Anonymous User or as user

I am trying to install the package boss but i am getting error below: Please advice install.packages("boss") --- Please select a CRAN mirror for use in this session --- CRAN mirror 1: 0-Cloud 2: Argentina (La Plata) 3: Argentina (Mendoza) 4: Australia (Canberra) 5: Australia (Melbourne) 6: Austria 7: Belgium 8:

Hi everyone Can anyone help? x = c("Treatment", "Planned", "Actual", "Demographics", "Outcomes") for (i in x) { df <- paste(i)[, c("Reference_ID", "Arm_ID")] unique(df) -> uniq as.data.frame(table(uniq$Reference_ID)) -> y i.Arms<- paste(y$Var1, y$Freq, sep="_") Print_Message("Check for the Total No of

I did a make update. I thought I was running the newest version of compiler-rt. But now I can't even get the project to build. I get the following error: i386-redhat-linux-gnu-clang++: clang/llvm/include/llvm/ADT/SmallVector.h:544: typename llvm::SmallVectorTemplateBase<T, llvm::isPodLike::value>::iterator llvm::SmallVectorImpl<T>::insert(typename

+kcc, llvmdev I think your compiler-rt checkout is out of date, because r188635 is supposed to fix that exact issue. On Mon, Aug 19, 2013 at 9:16 PM, Sharma, Yogesh < Yogesh.Sharma at saabsensis.com> wrote: > Sorry about that. I forgot a d:**** > > ** ** > > ldd (GNU libc) 2.12**** > > Copyright (C) 2010 Free Software Foundation, Inc.**** > > This is free

Sorry for re-posting the question, I did not get any reply. Kindly reply please if any one can. ### Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way

Hello R Users, Whether 'R' can import Netcdf format data files ?? Any package in 'R' that can help me on this front ?? Many thanks in advance, Regards, Yogesh -- =========================================== Yogesh K. Tiwari, Max-Planck Institute for Biogeochemistry, Postfach 10 01 64, D-07701 Jena, Germany Office : +49 3641 576376 Fax : +49 3641 577300 Home : +49

Hello R Users, I am a new user to R. When we make a simple plot then how to increase the font size of the data at the each axis. Many thanks, Kind regards, Yogesh -- =========================================== Yogesh Tiwari, Max-Planck Institute for Biogeochemistry, Hans-Knoell Strasse 10, D-07745 Jena, Germany Office : 0049 3641 576 376 Home : 0049 3641 223 163 Fax : 0049 3641

Hello, When I plot any data with simple plot command in R, for example :- plot(time,co2,ylim=c(350,380),xlim=c(1993,2003),xlab=NA,ylab=NA,type="p",col=5) Then the first value of x-axis(350) and y-axis(1993) never starts from origin, always they sifted from the origin. Is there any command that I can correct this in the ploted figure and both the axis values start from origin.

Dear R Users, I did not get any reply on my question so I am re-asking. This time I am giving sample data: 1 60.3162 -13.5993 -0.4353 46.0938 0.1877 -0.194E-07 2 60.3713 -13.5992 -0.4423 46.1241 0.2057 -0.231E-06 3 60.3430 -13.5981 -1.6163 44.9048 0.2237 -0.270E-06 4 60.3227 -13.5970 -2.6258 43.8785 0.2213

Dear R Users, I am using R 2.14.1 on windows How to read netcdf files in R ? Which packeges do we need to install for this, and what commands are used for reading netcdf files. Thanks, Best Regards, Yogesh Tiwari -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Centre for Climate Change Research, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone:

GNU ld version 2.20.51.0.2-5.36.el6 20100205 Copyright 2009 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) a later version. This program has absolutely no warranty. From: Kostya Serebryany [mailto:kcc at google.com] Sent: Monday, August 19, 2013 5:36 AM To: Sergey Matveev Cc: