User: sina.nassiri

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sina.nassiri20
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Switzerland/Lausanne
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2 days, 4 hours ago
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Posts by sina.nassiri

<prev • 6 results • page 1 of 1 • next >
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Comment: C: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
... "The key point is that this calibration formula was derived using only Affymetrix data, and therefore cannot be used to convert RNAseq-based ESTIMATE score to tumor purity" ... How does this not answer the question? ...
written 3 months ago by sina.nassiri20
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Answer: A: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
... The ESTIMATE algorithm (Yoshihara et al. 2013 Nature Communications) is comprised of two steps. **In the first step**, an enrichment score is calculated using single-sample GSEA (Barbie et al. 2009 Nature). Note that although immune cells are essentially part of the stroma, Yoshihara et al. calculat ...
written 6 months ago by sina.nassiri20
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Answer: A: What file formats requires for WGCNA ??
... Have you looked at WGCNA documentation? [https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/][1] Generally speaking, the initial input is a "properly normalized" gene expression matrix where rows represent genes and columns represent samples. Proper normalization depends on ...
written 8 months ago by sina.nassiri20
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Comment: C: Limma Analysis, BH Correction - adj. P-value all the same value
... Would have been helpful to provide the link to your post on bioconductor's webpage. ...
written 15 months ago by sina.nassiri20
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Answer: A: How does WGCNA decide which genes are connected?
... An adjacency matrix is a square, symmetric matrix with entries between 0 and 1 (don't have to be 1s and 0s), and the TOMsimilarity() and TOMdist() functions in WGCNA both handle non-binary adjacency matrices. ...
written 17 months ago by sina.nassiri20
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Answer: A: What is `soft thresholding` with WGCNA?
... In a weighted network (as is the case in WGCNA) all genes (nodes) are connected to one another. The idea behind soft thresholding (raising similarity measures to a power) is to emphasize more on stronger associations (larger correlation coefficients). The intuitive logic behind soft thresholding is ...
written 17 months ago by sina.nassiri20

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