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Yichuan's work journal

The scentific works of Yichuan for Bioinformatics/Computational Biology. Monday, April 30, 2012. Differential expression in RNA-seq analysis/microarray. Several methods have been applied and none of them is perfect. The major problem is the determination of major isoform in transcriptome assembly process, similar exon may switch the top1/2 hits. The results still not consisted with Cuffdif. Pipeline code may works:. Over - read.table("testing.tab",header=TRUE,sep=" t",row.names=1). A protocal replace PCR?

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Yichuan's work journal | yichuanliu.blogspot.com Reviews
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The scentific works of Yichuan for Bioinformatics/Computational Biology. Monday, April 30, 2012. Differential expression in RNA-seq analysis/microarray. Several methods have been applied and none of them is perfect. The major problem is the determination of major isoform in transcriptome assembly process, similar exon may switch the top1/2 hits. The results still not consisted with Cuffdif. Pipeline code may works:. Over - read.table(testing.tab,header=TRUE,sep= t,row.names=1). A protocal replace PCR?
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Yichuan's work journal | yichuanliu.blogspot.com Reviews

https://yichuanliu.blogspot.com

The scentific works of Yichuan for Bioinformatics/Computational Biology. Monday, April 30, 2012. Differential expression in RNA-seq analysis/microarray. Several methods have been applied and none of them is perfect. The major problem is the determination of major isoform in transcriptome assembly process, similar exon may switch the top1/2 hits. The results still not consisted with Cuffdif. Pipeline code may works:. Over - read.table("testing.tab",header=TRUE,sep=" t",row.names=1). A protocal replace PCR?

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1

Yichuan's work journal: April 2012

http://yichuanliu.blogspot.com/2012_04_01_archive.html

The scentific works of Yichuan for Bioinformatics/Computational Biology. Monday, April 30, 2012. Differential expression in RNA-seq analysis/microarray. Several methods have been applied and none of them is perfect. The major problem is the determination of major isoform in transcriptome assembly process, similar exon may switch the top1/2 hits. The results still not consisted with Cuffdif. Pipeline code may works:. Over - read.table("testing.tab",header=TRUE,sep=" t",row.names=1).

2

Yichuan's work journal: Models for Transcript Quantification from RNA-Seq

http://yichuanliu.blogspot.com/2011/07/models-for-transcript-quantification.html

The scentific works of Yichuan for Bioinformatics/Computational Biology. Thursday, July 7, 2011. Models for Transcript Quantification from RNA-Seq. RNA-seq is still a under-developed technology, the basic problem is to determine the abundances of the reads to transcriptome. The following is a review paper (28 pages.be careful! To issue multiple models to measure the relative transcript abundances from the sequenced reads. Subscribe to: Post Comments (Atom). View my complete profile.

3

Yichuan's work journal: Some recent developed tools for RNA-seq

http://yichuanliu.blogspot.com/2011/05/some-recent-developed-tools-for-rna-seq.html

The scentific works of Yichuan for Bioinformatics/Computational Biology. Tuesday, May 17, 2011. Some recent developed tools for RNA-seq. Isoform identification seems become hot in the area recently. 1) NSMAP: https:/ sites.google.com/site/nsmapforrnaseq. A Nonnegativity and Sparsity constrained Maximum A Posteriori (NSMAP) model is proposed to estimate the expression levels of isoforms from RNA-Seq data without the annotation information. 2) IsoEM: http:/ dna.engr.uconn.edu/software/IsoEM/. Simulation ex...

4

Yichuan's work journal: RNA-seq data needs normalization too!!!

http://yichuanliu.blogspot.com/2011/06/rna-seq-data-needs-normalization-too.html

The scentific works of Yichuan for Bioinformatics/Computational Biology. Friday, June 3, 2011. RNA-seq data needs normalization too! When examining large datasets processed from four different studies, researchers at Johns Hopkins and Brown Universities found RNA-seq data to be affected by similar errors that originally plagued the development of microarrays as a tool for analyzing gene expression. Also a review paper from Harvard published in Nature. Subscribe to: Post Comments (Atom).

5

Yichuan's work journal: Differential expression in RNA-seq analysis/microarray

http://yichuanliu.blogspot.com/2012/04/differential-expression-in-rna-seq.html

The scentific works of Yichuan for Bioinformatics/Computational Biology. Monday, April 30, 2012. Differential expression in RNA-seq analysis/microarray. Several methods have been applied and none of them is perfect. The major problem is the determination of major isoform in transcriptome assembly process, similar exon may switch the top1/2 hits. The results still not consisted with Cuffdif. Pipeline code may works:. Over - read.table("testing.tab",header=TRUE,sep=" t",row.names=1).

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Yichuan's work journal

The scentific works of Yichuan for Bioinformatics/Computational Biology. Monday, April 30, 2012. Differential expression in RNA-seq analysis/microarray. Several methods have been applied and none of them is perfect. The major problem is the determination of major isoform in transcriptome assembly process, similar exon may switch the top1/2 hits. The results still not consisted with Cuffdif. Pipeline code may works:. Over - read.table("testing.tab",header=TRUE,sep=" t",row.names=1). A protocal replace PCR?

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