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Title: | Constrained standardization of count data from massive parallel sequencing | Authors: | VAN HOUTVEN, Joris Cuypers, Bart Meysman, Pieter HOOYBERGHS, Jef Laukens, Kris VALKENBORG, Dirk |
Issue Date: | 2021 | Abstract: | In high-throughput omics disciplines like transcriptomics, researchers face a need to assess the quality of an experiment prior to an in-depth statistical analysis. To efficiently analyze such voluminous collections of data, researchers need triage methods that are both quick and easy to use. Such a normalization method for relative quantitation, CONSTANd, was recently introduced for isobarically-labeled mass spectra in proteomics. It transforms the data matrix of abundances through an iterative, convergent process enforcing three constraints: (I) identical column sums; (II) each row sum is fixed (across matrices) and (III) identical to all other row sums. In this study, we investigate whether CONSTANd is suitable for count data from massively parallel sequencing, by qualitatively comparing its results to those of DESeq2. Further, we propose an adjustment of the method so that it may be applied to identically balanced but differently sized experiments for joint analysis. We find that CONSTANd can process large data sets with about 2 million count records in less than a second whilst removing unwanted systematic bias and thus quickly uncovering the underlying biological structure when | Keywords: | Normalization;RNA-seq;transcriptomics;proteomics;multi-omics | Document URI: | http://hdl.handle.net/1942/33813 | DOI: | 10.1101/2021.03.04.433870 | Rights: | 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. | Category: | O | Type: | Preprint |
Appears in Collections: | Research publications |
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File | Description | Size | Format | |
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CONSTANd RNAseq rev1.pdf | Non Peer-reviewed author version | 680.85 kB | Adobe PDF | View/Open |
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