Questions tagged [tmm]
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data visualization RNAseq : scaling data for PCA and cluster dendogram
I have count data from a RNAseq experiment (2 samples are from normal cells and 3 samples are cells with a disease), and the data is already standardized by trimmed mean of M values (TMM).
I want to ...
- 81
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apply TMM on counts imported from salmon using Tximeta
I used Tximeta to import a summarisedExperiment from the salmon output (used with genocide transcriptome v34). I need to produce 4 matrix of counts:
- tx counts in TPM
- gene counts in TPM
- tx counts ...
- 37
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What is the formula for Mg values in TMM normalization for RNA Seq data?
I am reading through the paper "A scaling normalization method for differential expression analysis of RNA-seq data" by Mark D Robinson, Alicia Oshlack, available here.
In this paper they introduce a ...
- 111
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Error in quantile.default(x, p = p) in EgdeR calcNormFactors
I am trying to run TMM normalization using rpy2 and when I run calcNormFactors() function:
<...
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Convert TPM-normalized matrices back to UMI in python
I want to process a plenty of scRNAseq datasets in python, and I want to run TMM ...
- 2,538