Moderator: seidel
seidel ♦ 7.1k
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I work as a scientist at a non-profit research institute.
Posts by seidel
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... The simple approach: Select DE genes from each data set and examine their overlap via Venn diagram. Do genes DE overall overlap? Do genes in each category (up, down) overlap? You can evaluate the significance of overlap using a hypergeometric distribution or fisher test (see the help for phyper() if ...
written 8 months ago by
seidel ♦ 7.1k
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... Maybe some information is required as to what exactly you're trying to accomplish. If the ranges will be identical between each GRanges object you are creating, then you already have a set of reference ranges on which to score each tool, and each GRanges instance contains the results for that tool, ...
written 10 months ago by
seidel ♦ 7.1k
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... Sorry about that. I updated the references. ...
written 10 months ago by
seidel ♦ 7.1k
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... Your graphic is cut off - so we can only see what's happening in the top portion of your heat map - but assuming the pattern is preserved in the unseen portion, the simple answer is that the averages of the columns making up C3 are more similar to those of C2 and C4 than to C1, so the dendrogram was ...
written 10 months ago by
seidel ♦ 7.1k
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... The simplest answer would be to use the Poisson distribution. Assuming your data is normalized for read depth, you have a background estimate for your window of interest (lambda = 50), and an observed count for that window in your IP (1000), so in R you could estimate this with:
ppois(100, lamb ...
written 10 months ago by
seidel ♦ 7.1k
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932
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... Can't you just grep for the gene name of interest and redirect the output to a file? All the lines relevant to that gene should have the ID, and this would select and place all lines with the given gene id into a single file. ...
written 14 months ago by
seidel ♦ 7.1k
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... Yes...assuming the same set of transcripts is quantified between experiments, and the the non-zero count transcripts are identical between sets (i.e. the set of "expressed" transcripts is the same between conditions). In the case above, we both both different conditions AND different transcriptomes. ...
written 14 months ago by
seidel ♦ 7.1k
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... You want to convert "15:" to ">"? Or in general, do you want to convert anything to the left of the colon, including the colon, to ">"? For any number of lines in a file? There are ways to do both. One could easily use sed, or awk, or perl, with a one-liner (so no real script required), but as ...
written 19 months ago by
seidel ♦ 7.1k
7
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Answer:
A: Reproducing this plot in R
... Something like the following would work with base R functions:
# make some data
a <- data.frame(sample=paste0("A", 1:50), log10_total_counts=rnorm(50, 6))
# get x points
x <- 1:length(a$log10_total_counts)
# create plot, drop x axis
plot(x, a$log10_total_cou ...
written 19 months ago by
seidel ♦ 7.1k
3
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2
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2.9k
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2
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Answer:
A: Creating Count Matrix
... One suggestion using R would be:
# only return file names with a given pattern
dir(pattern="ReadsPerGene.out.tab")
# save the results to a variable
files <- dir(pattern="ReadsPerGene.out.tab")
counts <- c()
for( i in seq_along(files) ){
x <- read.tab ...
written 20 months ago by
seidel ♦ 7.1k
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