Questions tagged [normalization]

The tricky art of scaling quantitative data across libraries, typically to account for differences in sequencing depth. This can also be about scaling for read source length, like transcript or gene length, in order to enable comparisons across genes.

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3answers
226 views

RNASeq: Normalization, stabilization, gene length and rlog

I was thinking about the best method for normalization, which takes gene length into account (in order to compare genes)... Do you think I can do that? : - taking raw counts and dividing each gene by ...
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5answers
108 views

Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp) - almost 100 samples altogether. I have to use the samples data for ...
6
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1answer
932 views

Order of batch effects removal, data imputation and library size normalization in scRNA-seq data

I am preprocessing scRNA-seq data. What is the best practice in use to run both ComBat for batch effects removal, data imputation (to mitigate dropout) and library size normalization? I thought that ...
8
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1answer
3k views

How to apply upperquartile normalization on RSEM expected counts?

I see that TCGA RNASeq V2 RSEM data is normalized with upper-quartile normalization. After doing Quantification with RSEM with the samples I have, I got "genes.results" as output which has gene id, ...
13
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2answers
3k views

Normalization methods with RNA-Seq ERCC spike in?

ERCC spike-in is a set of synthetic controls developed for RNA-Seq. I'm interested in using it to normalize my RNA-Seq samples. In particular, I'd like to use the spike-ins to remove technical bias ...
6
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1answer
611 views

Drawbacks of upper quartile normalization for scRNA-seq data

I would like to use Upper Quartile normalization for scRNA-seq data defined as: The upperquartile (UQ) was proposed by (Bullard et al. 2010). Here each column is divided by the 75% quantile of the ...
11
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1answer
857 views

How to read and interpret a gene expression quantification file?

I have a gene expression quantification file from TCGA that contains the following lines: ...
3
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1answer
300 views

Large dataset normalization for PCA

I need to normalize a large (400Mb) dataset for doing PCA analysis. I want to use scran for doing that: ...
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0answers
49 views

GWAS phenotype data format and preprocessing

I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input. I have control and ...