User: ysdel

gravatar for ysdel
ysdel30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
8 months, 1 week ago
Joined:
2 years, 5 months ago
Email:
y***********@gmail.com

Posts by ysdel

<prev • 16 results • page 1 of 2 • next >
0
votes
2
answers
4.2k
views
2
answers
Comment: C: [DESeq2] time series strain-specific differences over time
... I'm sorry, I wasn't clear in what the problem is. Suppose I have results res1, res2, res3 from correlated tests. And I am interested in genes that satisfy the alternative hypothesis for all of these tests. So I will have to do hits = (res1$padj<0.05) & (res2$padj<0.05) & (res3$padj< ...
written 8 months ago by ysdel30
0
votes
2
answers
4.2k
views
2
answers
Comment: C: [DESeq2] time series strain-specific differences over time
... I am interested in genes that are DE at each time point (i.e. ALL time points) with respect to 0. I ran some simulations for the lm model at http://rpubs.com/ysdel/corpvals and it seems that the tests are correlated. I don't know how to think about this correctly to find the significance levels. ...
written 8 months ago by ysdel30
0
votes
2
answers
4.2k
views
2
answers
Comment: C: [DESeq2] time series strain-specific differences over time
... So if we do results(dds, contrast=list(c("strain_mut_vs_wt","strainmut.minute15"))) and then results(dds, contrast=list(c("strain_mut_vs_wt","strainmut.minute30"))) and on and on and then just select the genes that have an adjusted pvalue less than some threshold for all these tests, would thi ...
written 8 months ago by ysdel30
3
votes
1
answer
271
views
1
answer
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
... I am using DESeq2 for RNAseq analysis. I have 3 conditions (Control, Treatment 1, and Treatment 2). I gave the design matrix formula as ~  replicate + condition. And I get two sets of results as res1 <- results(dds, contrast=c('condition','control','t1')) res2 <- results(dds, contrast=c('con ...
rnaseq deseq deseq2 written 8 months ago by ysdel30
0
votes
3
answers
4.2k
views
3
answers
Comment: C: Batch correction in DESeq2
... Thank you. Well, plotCounts plots the counts for a single gene, so yes, you can see the batch effects and the treatment effect in the counts. But I was thinking of a way to look at the (all/top) genes like plotPCA does and conclude aha! DESeq2 correctly modeled/removed the batch effects so the log2f ...
written 8 months ago by ysdel30
0
votes
1
answers
771
views
1
answers
Comment: C: What problem does the MA plot diagnose? And how do you solve it?
... Thank you very much for explaining this! You're right, there are more up-regulated genes even after considering the Loess line, and there is plausible biological reason for this. I'm still curious though - the MA plot is supposed to detect some artifacts. When do those artifacts arise? ...
written 8 months ago by ysdel30
5
votes
1
answer
771
views
1
answer
What problem does the MA plot diagnose? And how do you solve it?
... I have an RNASeq experiment, and I am using DESeq2. After I get the results, I plot the MA plot. This is the output of plotMA: And this is my attempt at the MA plot: res$significant = (res$padj < .05) res$significant = as.factor(res$significant) res$significant[is.na(res$signific ...
rnaseq deseq deseq2 written 8 months ago by ysdel30 • updated 8 months ago by Ryan C. Thompson6.1k
0
votes
3
answers
4.2k
views
3
answers
Comment: C: Batch correction in DESeq2
... I agree, that is the way DESeq handles batch effects. Is there a way to visualize or diagnose how the batch effects were modeled? For example, I can do plotPCA(rlog(dds)) to plot the PCA showing the batch effects. I model the effects as ~ condition + replicate and compute the results. Now I'd like s ...
written 8 months ago by ysdel30
0
votes
0
answers
3.2k
views
0
answers
Comment: C: Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
... If I remove all multi-mapped reads, are the estimates of differential expression still valid. If certain regions of a gene are copies, then all reads mapping exlcusively to them will be ignored. Since this will affect all condtions equally, I am assuming that the estimate of log fold change should b ...
written 2.4 years ago by ysdel30
0
votes
0
answers
3.2k
views
0
answers
Comment: C: Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
... What about http://deweylab.biostat.wisc.edu/rsem/ ? ...
written 2.4 years ago by ysdel30

Latest awards to ysdel

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 175 users visited in the last hour