NOISeq

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 Next Generation Sequencing (NGS) technologies are increasingly being used for gene expression pro filing as a Next Generation Sequencing (NGS) technologies are increasingly being used for gene expression pro filing as a
-replacement for microarrays. The expression level given by these technologies is the number of reads in the library mapping to a given feature (gene, exon, transcript, etc.), i.e., the read counts. Most of the statistical methods for assessment of differential expression using count data rely on parametric assumptions about the distribution of the counts (Poisson, Negative Binomial, ...). Moreover, many of them need replicates to work and tend to have problems to evaluate differential expression in features with low counts.+replacement for microarrays. The expression level given by these technologies is the number of reads in the library mapping to a given feature (gene, exon, transcript, etc.), i.e., the read counts. Most of the statistical methods for assessment of differential expression using count data rely on parametric assumptions about the distribution of the counts (Poisson, Negative Binomial, ...). 
  
-NOISeq is a non-parametric approach for the identification of differentially expressed genes from count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. ​+ 
 +**NOISeq** is a non-parametric approach for the identification of differentially expressed genes from count data or previously normalized ​count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. ​
 This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression.
  
-The are two variants of the method: NOISeq-real uses replicateswhen availableto compute + 
-the noise distribution andNOISeq-sim simulates them in absence of replication. It should be noted that+NOISeq was tested on data sets with technical replicates. ​The are two variants of this method: NOISeq-real uses replicates when available to compute the noise distribution and NOISeq-sim simulates them in absence of replication. It should be noted that
 the NOISeq-sim simulation procedure assimilates to technical replication and does not reproduce biological the NOISeq-sim simulation procedure assimilates to technical replication and does not reproduce biological
 variability,​ which is necessary for population inferential analysis. ​ variability,​ which is necessary for population inferential analysis. ​
  
-Please, find {{:​posternoiseq_2010.pdf|here}} an outline of the NOISeq method. 
  
-NOISeq method ​has been implemented ​in R language.+Please, find {{:​posternoiseq_2012.pdf|here}} an outline of the NOISeq method
 + 
 +**NOISeqBIO** is the adaptation of NOISeq to handle biological variability. You can find a description of the NOISeqBIO method in this {{:​noiseqbio_techreport.pdf|Technical Report}} and also a summary ​in this {{:​posternoiseqbio.pdf|poster}}.
  
  
 +Both NOISeq and NOISeqBIO are included in [[http://​www.bioconductor.org/​packages/​release/​bioc/​html/​NOISeq.html|R/​Bioconductor NOISeq package]] together with a set of graphical tools to assess the quality of sequencing count data.
  
-====== References ====== 
-  * Bullard J.H., Purdom E., Hansen K.D. and Dudoit S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments. //BMC Bioinformatics//​ 11(1):94+. 
-  * Mortazavi A., Williams B.A., McCue K., Schae er L. and Wold B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. //Nature Methods// 5(7):​621-628. 
-  * Robinson M.D. and Oshlack A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. //Genome Biology// 11(3):R25+. 
  
  
  
-====== Contact ====== 
-NOISeq has been developed at the [[http://​bioinfo.cipf.es|Bioinformatics and Genomics Department]] of the [[http://​www.cipf.es|Centro de Investigación Príncipe Felipe]], in collaboration with the Department of Applied Statistics, Operations Research and Quality of the [[http://​www.upv.es|Universidad Politécnica de Valencia]], Spain. 
  
-Please, contact us at: 
  
-**Ana Conesa**, aconesa@cipf.es 
  
-**Sonia Tarazona**, starazona@cipf.es 
  
  
-====== How to cite us ====== 
  
-Tarazona S., García-Alcalde F., Ferrer A., Dopazo J., and Conesa A. **Differential expression in RNA-seq: a matter of depth**. (submitted)