Moderator: seidel

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seidel7.0k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Answer: A: How to compare two sets of results from Limma?
... 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 5 months ago by seidel7.0k
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Comment: C: GRanges: merge metadata from the same ranges
... 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 6 months ago by seidel7.0k
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Comment: C: how to compare the difference of read counts in a given region
... Sorry about that. I updated the references. ...
written 7 months ago by seidel7.0k
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Answer: A: Euclidean Clustering and pattern confusion
... 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 7 months ago by seidel7.0k
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Answer: A: how to compare the difference of read counts in a given region
... 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 7 months ago by seidel7.0k
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Comment: C: How to create custom gtf annotation file?
... 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 10 months ago by seidel7.0k
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Comment: C: Can I compare TPM values for a transcript across different transcriptome assembl
... 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 10 months ago by seidel7.0k
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Comment: C: Seeking for a Linux based script ?
... 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 16 months ago by seidel7.0k
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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 16 months ago by seidel7.0k
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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 16 months ago by seidel7.0k

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