Question: DESeq error of my data?
0
gravatar for barrypraveen
2.1 years ago by
barrypraveen20
barrypraveen20 wrote:

I am doing RNASeq analysis my pipe line is bowtie>tophat>htseq>DESeq. I have two conditions and two replicates of each condition. R version 3.3.2

library(DESeq2)

countsTable <- read.delim("crassa_merged_A_G.txt")

countsTable <- countsTable[,-1]

conditions <- factor(c("arabinose","arabinose","glucose","glucose"))

library(DESeq)

countDataSet <- newCountDataSet(countsTable, conditions)

countDataSet <- estimateSizeFactors(countDataSet)

sizeFactors(countDataSet)

head(counts(countDataSet))

head(counts(countDataSet,normalized=TRUE))

countDataSet <-estimateDispersions(countDataSet)

fpkm(countDataSet, robust = TRUE)

plotDispEsts(countDataSet)

dev.off()

plotDispEsts <- function(countDataSet){ plot(rowMeans( counts( countDataSet, normalized=TRUE ) ), fitInfo(countDataSet) $perGeneDispEsts, pch = '.', log="xy", ylab ="dispersion", xlab ="mean of normalized counts") xg = 10^seq( -.5, 5, length.out=300 ) lines( xg, fitInfo(countDataSet)$dispFun( xg ), col="red" )}

Error: unexpected symbol in "plotDispEsts <- function(countDataSet){plot(rowMeans(counts(countDataSet,normalized=TRUE) ),fitInfo(countDataSet)$perGeneDispEsts, pch='.',log="xy", ylab="dispersion",xlab="mean of normalized "

I am getting an error like that. please tell me

rna-seq R software error • 737 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by barrypraveen20
2

Why are you trying to rewrite the plotDistEsts function ? That's weird.

Anyway, you forgot the newline characters (or alternatively the semicolons). This should work :

plotDispEsts2 <- function(countDataSet){
    plot(rowMeans( counts( countDataSet, normalized=TRUE ) ), fitInfo(countDataSet) $perGeneDispEsts, pch = '.', log="xy", ylab ="dispersion", xlab ="mean of normalized counts")
    xg = 10^seq( -.5, 5, length.out=300 )
    lines( xg, fitInfo(countDataSet)$dispFun( xg ), col="red" )
}
ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Carlo Yague4.4k
2

Why are you trying to rewrite the plotDistEsts function

I doubt whether that's what he really wants to do.

ADD REPLYlink written 2.1 years ago by WouterDeCoster38k

Thanks for your reply and valuable suggestion. It works now.

ADD REPLYlink written 2.1 years ago by barrypraveen20
2

Not a solution, but a suggestion: since your pipeline includes htseq as a counting algorithm, why don't you simplify your pipeline using the built-in function for htseq in DESeq2?

DESeqDataSetFromHTSeqCount(sampleTable, directory = ".", design, ignoreRank = FALSE, ...)

This will create a seqExpressionSet already perfectly set for the DESeq() function.

Make sure to post the complete error message.

I associate myself in this request.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Macspider2.8k

Please use code formatting using the 101010 button. Select your code block, then click 101010.

Make sure to post the complete error message.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by WouterDeCoster38k
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