 | | Normalization of imported RNA-seq data | | | Question | | RNASeq analysis sometimes produces e.g. .tsv files with several different normalizations. Which normalization should I use for analysis in Qlucore?
Note that from Qlucore Omics Explorer 3.10 there is integrated support for DESeq2 methods in the program.
| | Answer | Definitions:
* Raw Counts: Raw (integer) counts per gene and sample.
* Normalized Counts: Normalized (real) counts per gene and sample scaled to the sequencing depth by DESeq2.
* VST Blind Counts: Counts on a log2 scale per gene and sample after variance stabilizing transformation (VST) disregarding the generalized linear model design.
* VST Model Counts: Counts on a log2 scale per gene and sample after variance stabilizing transformation (VST) considering the generalized linear model design.
* FPKMs: Fragments Per Kilobase Per Million.
Use
* Raw Counts if you want to use the normalizations available in Qlucore (FPKM/TPM/TMM).
* VST Blind Counts if you want to use the VST normalization from DESeq2.
* VST Model Counts if you know which model was used with DESeq2 and want to use that. An alternative approach is to use VST Blind Counts normalization + eliminated factors in Qlucore.
* FPKM requires log transform of data. It is preferable to instead use the raw counts + the FPKM in Qlucore since the software then will handle the log transformation.
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