User: Bioinformatics_NewComer

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Posts by Bioinformatics_NewComer

<prev • 131 results • page 1 of 14 • next >
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Comment: C: output TMM normalized counts with edgeR
... I've code and analysis pipeline developed on my end employing edgeR, limma, voom and other utilities. I'm reading and exploring when to use what and why, thus I thought to nudge this post because I'm confused and cannot understand further. Anyway, thanks~ ...
written 6 weeks ago by Bioinformatics_NewComer320
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Comment: C: output TMM normalized counts with edgeR
... The end goal is simple differential gene expression analysis using case-control (human tissue). ...
written 6 weeks ago by Bioinformatics_NewComer320
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Comment: C: How to adjust data for "continuous" covariates ?
... https://bioinformatics.stackexchange.com/questions/9172/how-are-residuals-used-as-new-phenotype This may be of help to you. ...
written 6 weeks ago by Bioinformatics_NewComer320
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Comment: C: output TMM normalized counts with edgeR
... It is a great informative post. Thanks. I think I'm a bit confused with normalization here though. When someone says or shares normalized data, do they share `cpm()` value or, They scale their gene counts by `norm.factors` to generate normalized gene counts? ...
written 6 weeks ago by Bioinformatics_NewComer320
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Comment: C: RMA signal values
... Sorry to wake this arcane thread. What does the VALUE column tell? I'm looking around in vain with no documentation or manual, dictionary to assist. ...
written 4 months ago by Bioinformatics_NewComer320
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Comment: C: What Are Phased And Unphased Genotypes?
... Hi - sorry to bump this ancient thread. I've been scratching my head over this for some time now. What does 01/00 mean? If an individual in 1000G (Phase 3), for SNP1 has 00 haplotype what does it tell? Thanks. ...
written 5 months ago by Bioinformatics_NewComer320
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Comment: C: How to adjust data for "continuous" covariates ?
... ## ... Now use lm1$residuals instead of dat$y Would you please be able to explain Why this residuals are used as new phenotype and how? ...
written 10 months ago by Bioinformatics_NewComer320
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R - snpmatrix - data filtering
... Hi all, I'm interested to use genegeneinteraction R package. For that data are read and a snp matrix is generated. When I try to run gene gene interaction I get error GGI.res <- GGI(Y=Y, snpX=data$snpX, genes.info=data$genes.info,method="PCA") Error: > Error in GGI(Y = Y, snpX = data ...
matrix snp written 15 months ago by Bioinformatics_NewComer320
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Comment: C: Help with SnpMatrix in R
... The link is dead. Am too looking for help with snpmatrix. ...
written 15 months ago by Bioinformatics_NewComer320
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Comment: C: Module merging WGCNA
... URL: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Consensus-NetworkConstruction-man.pdf Section 2.a.7, Page 9, merge = mergeCloseModules(multiExpr, unmergedLabels, cutHeight = 0.25, verbose = 3) Here, code merges modules that have close/similar expre ...
written 16 months ago by Bioinformatics_NewComer320

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