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8 votes
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How to apply upperquartile normalization on RSEM expected counts?

You can use the quantile function in base R to get the value of a particular quantile (e.g. 0.75 for the upper quartile). This can then be used as a factor for ...
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6 votes
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Missing genes and normalisation of RSEM output using EBSeq

Yes, that blog post does represent just one guy's opinion (hi!) and it does date all the way back to 2014, which is, like, decades in genomics years. :-) By the way, there is quite a bit of literature ...
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5 votes
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Duplicate genes with RSEM counts: Which one to choose?

Let's look into this a bit more deeply. For instance: HUGO: SOGA3 Ensembl 1: ENSG00000214338 Ensembl 2: ENSG00000255330 The Ensembl pages (linked above) for both ENSG00000214338 and ENSG00000255330 ...
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5 votes

Duplicate genes with RSEM counts: Which one to choose?

There is no one-to-one mapping of gene ids from one database to the other. Ensembl (who maintain Ensembl ENSG IDs), ncbi (who maintain EntrezGene IDs and RefSeq transcript ids) and HUGO (who maintain ...
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  • 3,201
3 votes

Is it possible to calculate p-values for fold changes of single replicate RNA-seq samples?

DESeq2 is able to adjust p-values for single-replicate samples by estimating shared dispersion across all samples. DESeq2 will give a warning, but try its best to carry out the analysis. More ...
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3 votes

Missing genes and normalisation of RSEM output using EBSeq

Include all genes/transcripts in your analysis. A transcript that is not detected could be undetected through sampling error (i.e. the sequencer / library prep just happened to miss that transcript), ...
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3 votes
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How to calculate fold change in gene expression from RSEM (RNAseq)

You should use a proper statistical framework for RNA-seq dfferential analysis (which includes FC calculation). Standard tools for this are (among others) edgeR or <...
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3 votes
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STAR quantMode vs RSEM vs Kallisto

STAR quantMode (GeneCounts) essentially provides the same output as HTSeq-Count would, ie. number of reads that cover a given gene. This is the most simple measure of expression you could get from RNA-...
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  • 437
2 votes
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Why I am getting different gene lengths for the same genes in different samples with rsem-calculate-expression?

If there are differences in the expression of individual transcripts between samples then both the length and effective length will differ between samples. It is commonly the case that the ratio of ...
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