Question: Normality test for rna seq data
0
gravatar for rhasanvandj
4 weeks ago by
rhasanvandj10
rhasanvandj10 wrote:

Hello friends I want to know how to test HT-Seq count data for normality in R? Any body has any idea? Thnx

rna-seq • 145 views
ADD COMMENTlink modified 4 weeks ago by ATpoint40k • written 4 weeks ago by rhasanvandj10
2
gravatar for ATpoint
4 weeks ago by
ATpoint40k
Germany
ATpoint40k wrote:

Fully agreeing on the comment of h.mon. RNA-seq data are not normally distributed. Plot a histogram of the counts and you will see it without any test. DESeq2 models counts as a negative binomial. There is no need to filter anything, check for any distribution (if you have standard RNA-seq data) or apply any outlier (or something else) correction. Please start with your raw HTseq counts and follow the DESeq2 manual. If there was the need for any actions to be taken it would be in the DESeq2 manual.

ADD COMMENTlink written 4 weeks ago by ATpoint40k

I see Thanks ATpoint

ADD REPLYlink written 4 weeks ago by rhasanvandj10
1
gravatar for h.mon
4 weeks ago by
h.mon31k
Brazil
h.mon31k wrote:

Please, provide more details and put some more effort in your question - for example, provide some background on why you want to perform these tests, what have you read so far, and so on.

It is widely known and accepted RNAseq count data does not follow a normal distribution, rather, it is better modeled as a negative binomial distribution. See some old posts:

Why Does Rna-Seq Read Count Fit Poisson Distribution?

Statistical Distributions In Rna-Seq Data Analysis

ADD COMMENTlink written 4 weeks ago by h.mon31k

Hi h.mon Thanks for responding. I want to do differential expression analysis (with DESeq2 package) and I was not sure if my HT-seq data is following normal distribution. Also I am not sure if the data is not normal it causes a problem when doing differential expression analysis. So, I wanted to get rid of outliers before doing analysis. What is your idea?

ADD REPLYlink written 4 weeks ago by rhasanvandj10
1

Please read the DESeq2 vignette, it tackles all your questions so far.

ADD REPLYlink written 4 weeks ago by h.mon31k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 767 users visited in the last hour