Question: Why less DE for non replicates
0
gravatar for manoharankumar01
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
ADD COMMENTlink modified 2.9 years ago by Devon Ryan92k • written 2.9 years ago by manoharankumar010
5

As always without any replicates it would be hard to draw conclusions.. IMO I would not trust the results..

ADD REPLYlink written 2.9 years ago by Nicolas Rosewick8.3k
3

We need to post this in a banner at the top of the page.

ADD REPLYlink written 2.9 years ago by Devon Ryan92k
4

Or just a helpful pop-up when making a post containing some keywords: https://cdn.meme.am/cache/instances/folder314/500x/73204314.jpg

ADD REPLYlink written 2.9 years ago by WouterDeCoster41k

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

ADD REPLYlink written 2.9 years ago by WouterDeCoster41k

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")

ADD REPLYlink written 2.9 years ago by manoharankumar010

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

ADD REPLYlink written 2.9 years ago by poisonAlien2.8k
1
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Fewer replicates means less power.

ADD COMMENTlink written 2.9 years ago by Devon Ryan92k
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