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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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Gene expression values using IsoformSwitchAnalyzeR #208

Closed Harshangda closed 4 months ago

Harshangda commented 11 months ago

The gene expression values I am getting from using IsformSwitchAnalyzeR (summing up isoform expression) are different from the values we get by doing normal differential gene expression (aligning reads to the gene using DESeq). Why is it so and which one is more accurate?

chunxubioinfor commented 7 months ago

Hi @Harshangda ! Compared with traditional gene quantification, transcript-level gene quantification, which IsoformSwitchAnalyzeR uses, has many advantages. One of them is the more accurate quantification algorithm (which includes correcting various sequence biases). For further information, please check the official documentation.. Let me know if you need more help :)