User: Jake

gravatar for Jake
Jake60
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60
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Trusted
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United States
Last seen:
1 month ago
Joined:
4 years, 6 months ago
Email:
j*******@gmail.com

Posts by Jake

<prev • 57 results • page 1 of 6 • next >
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Small differences in limma with and without contrast matrix
... Hi, I am doing pairwise RNA-Seq comparisons between 3 groups in limma. Looking at the manual it seems like this is best done with the contrasts. However, I wanted to compare the results using contrasts with the results doing just group 1 vs group 2 in limma. I've noticed some differences in the dif ...
limma written 5 weeks ago by Jake60 • updated 5 weeks ago by Aaron Lun24k
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Normalize for changes in one direction
... Hi, I'm trying to measure RNA stability changes after knocking out a repressor RNA binding protein. I'm using 4sU to label nascent RNA and also collecting total RNA as per this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114636/. I can then calculate RNA stability by the ratio of nascent RN ...
rnaseq limma voom written 17 months ago by Jake60 • updated 17 months ago by Aaron Lun24k
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Comment: C: Non-used samples changing number of significant genes in limma
... I tried it with both voomWithQualityWeights and voomWithQualityWeights(var.design = design). This is what the plot looks like for the second one: https://imgur.com/HDhOUhQ. The order is: ko 1 high ko 1 low ko 1 mono ko 2 high ko 2 low ko 2 mono wt 1 high wt 1 low wt 1 mono wt 2 high wt ...
written 21 months ago by Jake60
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Non-used samples changing number of significant genes in limma
... Hi, I performed polysome profiling to measure translation rate in wildtype and knockout cells. For the polysome samples I collected a monosome fraction, a low polysome fraction, and a high polysome fraction. I also collected mRNA for both wildtype and knockout. I'm interested in comparing translati ...
limma voom written 21 months ago by Jake60
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pintersect and psetdiff changed behavior
... Hi, I had code to extract exons, introns and exon-intron boundaries from about a year ago. However, when I went to re-run it I now get the following two errors. Did the behavior of these functions change? I'd like to take the range of exons in a gene (union of all isoforms) and define everything in ...
genomicranges written 2.3 years ago by Jake60 • updated 2.3 years ago by Michael Lawrence11k
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RNA-Seq metagene coverage
... Hi, I'd like to calculate RNA-Seq meta read coverage over different subsets of genes similar to the genebody coverage function in RSeQC (http://rseqc.sourceforge.net/#genebody-coverage-py). I saw a number of packages that will do this for genomic coordinates, but I'm looking for something that will ...
coverage written 3.0 years ago by Jake60
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Comment: C: RSEM expected counts to limma-voom
... They have both. I was interested in the gene quantification. ...
written 3.0 years ago by Jake60
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RSEM expected counts to limma-voom
... I'm interested in analyze some RNA-Seq data from Encode. They have posted a gene quantification file for each sample from RSEM. My understanding is that I can pass the expected counts to voom and then limma even though raw counts is more ideal. I just wanted to check that this is correct? Thanks ...
limma voom rsem written 3.0 years ago by Jake60 • updated 3.0 years ago by Gordon Smyth38k
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Answer: A: matchPWM on DNAStringSet rather than just one sequence?
... That works, but is incredibly slow once I start looping through all of my UTRs and even a few RNA binding proteins. Is there another bioconductor package or program outside that would be significantly faster? ...
written 3.1 years ago by Jake60
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matchPWM on DNAStringSet rather than just one sequence?
... I have a couple PWMs for RNA binding proteins and I also have the sequences of candidate UTRs in different groups as a DNAStringSet. I'd like to see how many of the UTRs (and which ones) in each group match a given PWM. However, it looks like the matchPWM function in Biostrings only supports a singl ...
biostrings written 3.1 years ago by Jake60

Latest awards to Jake

Popular Question 17 months ago, created a question with more than 1,000 views. For Check understanding of linear model
Popular Question 17 months ago, created a question with more than 1,000 views. For ribosome profiling analysis with different dispersions
Popular Question 17 months ago, created a question with more than 1,000 views. For Help with design matrix for two cell types, multiple treatments
Popular Question 17 months ago, created a question with more than 1,000 views. For RSEM expected counts to limma-voom
Popular Question 17 months ago, created a question with more than 1,000 views. For Best way to convert ensembl id to mgi?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Ribosome profiling analysis in DEseq2/limma
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Check understanding of linear model
Popular Question 2.3 years ago, created a question with more than 1,000 views. For bedtools like subtract in genomic ranges?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For limma-voom for miRNA seq
Popular Question 2.3 years ago, created a question with more than 1,000 views. For rtracklayer export GRangesList as gtf and change attributes
Popular Question 2.3 years ago, created a question with more than 1,000 views. For coverage over specific GenomicRanges
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ribosome profiling analysis with different dispersions
Popular Question 3.3 years ago, created a question with more than 1,000 views. For genomicfeatures rsqlite database or disk is full

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