User: Yury Bukhman

gravatar for Yury Bukhman
Yury Bukhman10
Reputation:
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Last seen:
2 years, 4 months ago
Joined:
10 years, 4 months ago
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y*******@glbrc.wisc.edu

Posts by Yury Bukhman

<prev • 13 results • page 1 of 2 • next >
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Comment: C: how to deal with technical replicates in limma camera
... Thanks a lot, Gordon! Yury ...
written 2.4 years ago by Yury Bukhman10
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how to deal with technical replicates in limma camera
... Hi, I have a dataset where each experimental condition has 3 biological replicates and each biological replicate has 2-3 technical replicates. When I use lmFit(), I can account for correlations between technical replicates using the correlation parameter. However, camera() does not seem to have suc ...
limma camera written 2.4 years ago by Yury Bukhman10 • updated 2.4 years ago by Gordon Smyth37k
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Comment: C: Mutation effect on expression (RNA-Seq) using limma
... Aaron, what would be a good way to assess the quality of limma model fits? ...
written 2.7 years ago by Yury Bukhman10
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Answer: A: Getting rawdata for TMM normalization
... You can rename data frame columns using function names or colnames. See example("names"). You can replace NA with 0 like so: > a <- c(1:3,NA) > a [1] 1 2 3 NA > a[is.na(a)] <- 0 > a [1] 1 2 3 0   ...
written 2.8 years ago by Yury Bukhman10
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Answer: A: Getting rawdata for TMM normalization
... Humberto, try head(s1). What do you see? If you haven't already done so, read the appropriate section of An Introduction to R on the R Project's web site: https://cran.r-project.org/doc/manuals/r-release/R-intro.html#The-read_002etable_0028_0029-function. Also try ?read.csv and example(read.csv). ...
written 2.8 years ago by Yury Bukhman10
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Comment: C: Getting rawdata for TMM normalization
... Try merge(x, y, by = "GeneID"). Sorry I forgot the quotes in my previous answer. Without the quotes, R thinks you are referring to an object in an environment, rather than a data frame column name. Here is a quick example: > x <- data.frame(gene_id = letters[1:3], count = (1:3)*100) > x ...
written 2.8 years ago by Yury Bukhman10
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Answer: A: Getting rawdata for TMM normalization
... Hi Humberto, You can format your 3 datasets as data frames with columns gene_id and count. You can then use R's merge function to combine them with parameter by = gene_id. You will need to use merge twice, merging first and second datasets first, then merging the result with the third dataset. This ...
written 2.8 years ago by Yury Bukhman10
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Comment: C: How to normalize chemical genomics barcode sequencing data
... Thanks again! Yury ...
written 2.9 years ago by Yury Bukhman10
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Comment: C: How to normalize chemical genomics barcode sequencing data
... Thanks, Aaron! This is very helpful. Looks like I can use diffSplice() to test if there are any genes where different mutants behave differently. Is it generally a good idea to aggregate data at gene level, e.g. by summing the counts? In particular, I am concerned that failing to do so would affect ...
written 2.9 years ago by Yury Bukhman10
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How to normalize chemical genomics barcode sequencing data
... Hello, I am trying to analyze a barcode sequencing dataset. The experimental technique that generates the data is described here: Chemical genomic profiling via barcode sequencing to predict compound mode of action. Briefly, we are sequencing a pool of gene knock-out mutants of a yeast or bacterium ...
sequencing normalization limma edger written 2.9 years ago by Yury Bukhman10 • updated 2.9 years ago by Aaron Lun23k

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