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Dear all, I need to make dendogram from read count in a csv file across 34 samples including biological replicate. Please share R code or package to do this. Do I also need to normalized read count before using read data? Thanks [[alternative HTML version deleted]]

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")

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 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 , I am trying to open vignette DESeq2 but getting below error: > vignette("DESeq2") > START /usr/bin/evince "/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf" Cannot parse arguments: Cannot open display: xdg-open: no method available for opening '/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf' -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological

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)

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]]