User: Elsa

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Elsa0
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Posts by Elsa

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Comment: C: annotatePeak() in ChIPseeker - how long does it take to run?
... Cool! Thanks!! ...
written 4.1 years ago by Elsa0
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Comment: C: annotatePeak() in ChIPseeker - how long does it take to run?
... Thanks Herve and Guangchuang for the tests, explanations and new implementations!! You are the best! :) How long will it take for the new updated version to become available in the "update" packages section of R? E. ...
written 4.1 years ago by Elsa0
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annotatePeak() in ChIPseeker - how long does it take to run?
... Hi, I have downloaded a chip-seq .bed file from an available geo dataset (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM590111) and would like to use ChIPseeker to plot the Average Profile of ChIP peaks binding to the TSS region of a specific group of genes. However, I cannot seem to pass th ...
chipseq chipseeker org.mm.eg.db txdb.mmusculus.ucsc.mm9.knowngene annotatepeak written 4.1 years ago by Elsa0 • updated 3.9 years ago by Martin Morgan ♦♦ 23k
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Comment: A: decideTests() options in LIMMA
... Thank you for the explanations! The underlying idea of using also the B stats emerged from the fact that, even using an adjusted p-value of lower than 0.01, we still have ~7000 differentially expressed genes... which is a lot! So, we starting wondering how we could trim down our data using other st ...
written 4.3 years ago by Elsa0
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decideTests() options in LIMMA
... I have applied lmFit to RNAseq data following the code below: ## Fit the model with counts data fit_counts = lmFit(eset_counts, design) fit_counts = eBayes(fit_counts) ## Use the contrast matrix to make the comparisons fit_counts_cont = contrasts.fit(fit_counts, contrast) fit_counts_cont = eBayes ...
limma b stats decidetests written 4.3 years ago by Elsa0

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For annotatePeak() in ChIPseeker - how long does it take to run?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For annotatePeak() in ChIPseeker - how long does it take to run?

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