User: emmasreid

gravatar for emmasreid
emmasreid20
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New User
Location:
United Kingdom
Last seen:
4 years, 5 months ago
Joined:
4 years, 6 months ago
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e********@btinternet.com

Posts by emmasreid

<prev • 5 results • page 1 of 1 • next >
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Comment: C: cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... This worked perfectly - thank you so much Max! Finally manged to pick up some CNVs after days of struggling. Thank you again for solving my problem! Cheers, Emma ...
written 4.5 years ago by emmasreid20
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Comment: C: cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... Hello! Just an update - I did as you suggested and did table(seqlevels(X)). This gave a value of '1' for all chromosome: chr1 chr10 chr11 ...etc.     1     1     1      ...etc.   I then tried the head(X[,1:3]) command to see if the counts are even being called correctly at all and got this: GRang ...
written 4.5 years ago by emmasreid20
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Comment: C: cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... Thank you! So I would use that code to determine which chromosome needs to be removed, and then I assume this line of code would need to be inserted somewhere: normalizeChromosomes(X, chr, normType = "poisson", qu = 0.25, ploidy) Any chance you could hazard a guess as to where I should put this (o ...
written 4.5 years ago by emmasreid20
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Comment: C: cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... Thank you so much for your swift reply! I think I understand your explanation of the problem - any ideas on the command(s) I should use instead to circumvent this problem?  (Apologies again for my ignorance - I've been struggling with this for days now...!) ...
written 4.5 years ago by emmasreid20
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cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... Hi all, Firstly, apologies if this is a daft/duplicated question - I am very new to this forum and data analysis using R in general. I am trying to analyse some gene panel data using the cn.mops package in R using the code provided under Section 6 of the package vignette ("Exome sequencing data"). ...
next generation sequencing R ngs cn.mops written 4.5 years ago by emmasreid20 • updated 4.5 years ago by Devon Ryan86k

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