Black,M.A. and Doerge,R.W. (2001) Calculation of the minimum number of replicate spots required for detection of signi(R)cant gene expression fold change in microarray experiments. Technical Report. Department of Statistics, Purdue University....
calculation is based on MCMC.Results: We applied GFOLD to five datasets (4 RNA-seq and 1 GRO-seq) with biological replicates and compared it with edgeR, DESeq, DEGseq, Poisson, Cufflinks and fold change with offset.Comparisons show that GFOLD outperforms all other methods in most cases ...
In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large d
We use total counts for the normalization of raw counts, to rectify the batch sequencing deptch. Because some sgRNAs in the reference have very low raw counts, which can affect the fold change calculation of the following analysis. We define sgRNAs counts less than 0.05 quantile both in refe...
(Fig.1b). Disruption of the stem loop by non-compensatory mutations is known to change gene expression7. To explore a possible regulation by RNA-binding proteins, we determined binding partners to this structure and applied our quantitative proteomics workflow comparing the wild-typePMA1hairpin to...
This is directly related with the methodology of the statistical score calculation and it is addressed on the paper to be published. Indeed, the directionality of the edges is the most important feature of the plot. The similarities are calculated for every pair of clusters from different datasets...
test, which is based on the analysis of the distribution of intensities of all features on a microarray mapped to a three dimensional feature space composed of the average difference of gene expression (logarithm of fold change), total variance and average expression level. it introduces a score...
The secondary structure constraint lossLss3dsubscript𝐿𝑠𝑠3𝑑L_{ss3d}that we propose is to encode secondary structural information directly into 3D prediction. In order to unify the calculation of different types of base pairing constraint in 3D space, we define four pseudo ato...
Signal fold-change controls pattern formation 来自 ResearchGate 喜欢 0 阅读量: 20 作者:MF Simsek,E Ozbudak 摘要: Oscillations are prevalent in natural systems. A gene expression oscillator, called the segmentation clock, controls segmentation of precursors of the vertebral column. Genes belonging to ...
Relative gene expression, normalized to beta-actin, and undifferentiated iPS cells, AFE, or human primary cell controls (ΔΔCt), was calculated as fold change using the 2(-ΔΔCt) method58. If undetected, a cycle number 40 was assigned to allow fold change calculation. The data are ...