User: Kevin Lee

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Kevin Lee • 40
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6 years, 7 months ago
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6 years, 7 months ago
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k*************@gmail.com

Posts by Kevin Lee

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Comment: C: ExomeCopy error
... Thanks Mike, I have now run exomeCopy to completion. Unfortunately, the output looks erroneous. The percent normal state is very low for all of the samples (around 10%). And consequently, when I visualize the plots using: cnv.cols <- c("red", "orange", "black", "deepskyblue", "blue") plotCom ...
written 6.6 years ago by Kevin Lee • 40
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ExomeCopy error
... Hello, I am working with ExomeCopy, and I cannot get past this error: fit.list <- lapply(sample.names, runExomeCopy, seqs) *Error in negLogLike(c(logit(goto.cnv), logit(goto.normal), beta.hat, log(phi.hat)), :* * NA/NaN/Inf in foreign function call (arg 5)* where: runExomeCopy <- function ...
exomecopy written 6.6 years ago by Kevin Lee • 40 • updated 6.6 years ago by Michael Love ♦ 26k
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Comment: C: DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infecte
... Hello Simon, I appreciate your assistance. A follow-up question: what is the appropriate method to handle a read that splits an exon junction and is therefore mapped to two exons when using a short read mapping software? Counting it as being present in both exons seems to give undue weight to the ...
written 6.6 years ago by Kevin Lee • 40
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DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood
... Hello, My name is Kevin Lee, and I am a PhD candidate in Bioinformatics at Georgia Institute of Technology. I have been trying to decide between various normalization techniques for RNA-seq methods for a parasite infection time-course study. The RNA-seq data that I will have will be from infected ...
normalization deseq dexseq written 6.6 years ago by Kevin Lee • 40 • updated 6.6 years ago by Simon Anders • 3.6k

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