inst/extdata/filtering.md
In OceaneCsn/DIANE: DIANE
Removing low count genes
Removing genes with very low aboundance is a common practice in RNA-Seq analysis pipelines for several reasons :
-
They have little biological signifiance, and could be caused either by noise or mapping errors.
-
The statitical modelling we are planning to perform next is not well suited for low counts, as they make the mean-variance relationship harder to estimate.
There is no absolute and commonly accpeted threshold value, but it is recommended to allow only genes with more than 10 counts per sample in average. DIANE thus proposes a threshold at 10*sampleNumber, but feel free to experiment with other values depending on your dataset.
OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.
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Removing low count genes
Removing genes with very low aboundance is a common practice in RNA-Seq analysis pipelines for several reasons :
-
They have little biological signifiance, and could be caused either by noise or mapping errors.
-
The statitical modelling we are planning to perform next is not well suited for low counts, as they make the mean-variance relationship harder to estimate.
There is no absolute and commonly accpeted threshold value, but it is recommended to allow only genes with more than 10 counts per sample in average. DIANE thus proposes a threshold at 10*sampleNumber, but feel free to experiment with other values depending on your dataset.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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