Question: Differetial analysis after HTSEq count
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gravatar for rob.costa1234
3.5 years ago by
rob.costa1234200
United States
rob.costa1234200 wrote:

What is the best tool/ software or method to perform a statistical analysis on HTseq count data . I s it simply performing aova or t tests or ay sophisticate methods like edgeR / DEseq which take raw reads?

Thanks

rna-seq • 1.1k views
ADD COMMENTlink modified 3.5 years ago by Antonio R. Franco4.4k • written 3.5 years ago by rob.costa1234200

DEseq models the read count distribution and provides a robust comparison in comparison to a simple t-test or anova

ADD REPLYlink written 3.5 years ago by vakul.mohanty240

edgeR/DESeq/DESeq2/etc don't take raw reads. They take gene read counts from tools like HTseq-count or featureCounts.

ADD REPLYlink written 3.5 years ago by Chris Cole740
1
gravatar for Antonio R. Franco
3.5 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.4k wrote:

I would say that the reference methods for running DE analysis nowadays are those using DESeq2 /edgeR and the like because they assume a determined distribution of the data and use a linear model fit which are far more robust that a simple anova or t-test

ADD COMMENTlink written 3.5 years ago by Antonio R. Franco4.4k
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