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How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
11 days ago • updated 6 days ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
130
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 5 days ago by
Gordon Smyth
45k • written 5 days ago by
mohammedtoufiq91
▴ 10
1
vote
1
reply
73
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 5 days ago by
ATpoint
★ 1.2k • written 5 days ago by
Dimitris
• 0
1
vote
3
replies
79
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R
edgeR
updated 1 day ago by
Gordon Smyth
45k • written 1 day ago by
Mohamed
• 0
1
vote
2
replies
114
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
10 days ago • updated 3 days ago
takemoto
• 0
0
votes
6
replies
166
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
6 days ago • updated 5 days ago
nabiyogesh
▴ 10
6 results • Page
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Comment: Italicise
by
Kevin Blighe
3.5k
Okay, I am guessing that the problem is that you need to update the version of *EnhancedVolcano* to the latest version. Can you try that? T…
Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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