Question: Why less DE for non replicates
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2.9 years ago by
manoharankumar010 wrote:

Hi,

I have been working with human and mouse organisms with non replicates, I am getting less number of DE genes using different method DESeq. Below is the total read count for two samples.

human: sample1: 22905420 sample2: 23715800 total genes: 25,370 DE genes: 97

I am trying to understand why did i get less DE genes? Could someone help me?

Thanks.

rna-seq • 758 views
modified 2.9 years ago by Devon Ryan92k • written 2.9 years ago by manoharankumar010
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As always without any replicates it would be hard to draw conclusions.. IMO I would not trust the results..

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Please be more informative with regard to the experimental setup and the commands you used, don't make us guess.

Sorry, I have used following commands:

library(DESeq)

data = read.table("DEinput.txt", header=T, row.names=1, com='') col_ordering = c(1,2) rnaseqMatrix = data[,col_ordering] rnaseqMatrix = round(rnaseqMatrix) rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,] conditions = factor(c(rep("s1", 1), rep("s2", 1)))

exp_study = newCountDataSet(rnaseqMatrix, conditions) exp_study = estimateSizeFactors(exp_study) exp_study = estimateDispersions(exp_study, method="blind", sharingMode="fit-only")

res = nbinomTest(exp_study, "s1", "s2")

You don't have replicates. Hence, test is limited in degrees of freedom to estimate variance and thereby less power to detect DE genes.

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2.9 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Fewer replicates means less power.