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RNAseq123
•
reset
12
votes
4
replies
4.8k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.8 years ago by
Gordon Smyth
51k • written 7.4 years ago by
wd
▴ 30
5
votes
6
replies
3.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.6 years ago
Alan
• 0
2
votes
1
reply
1.2k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.4 years ago by
Gordon Smyth
51k • written 2.4 years ago by
Mikołaj Mierzejewski
• 0
2
votes
5
replies
1.3k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 23 months ago by
Gordon Smyth
51k • written 23 months ago by
Istvan Albert
▴ 50
1
vote
1
reply
594
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
kaurprab
• 0
1
vote
3
replies
5.2k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 3.8 years ago by
mmicky5050
• 0
1
vote
1
reply
1.8k
views
featureCounts running too long
RNAseq123
updated 9 months ago by
difraiadomenico
• 0 • written 3.7 years ago by
demirkalecy
▴ 10
1
vote
6
replies
4.3k
views
KEGG enrichment analysis for non model organism
RNAseq123
23 months ago
afsanarupa1
• 0
1
vote
1
reply
914
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.2 years ago by
ATpoint
★ 4.5k • written 2.2 years ago by
Mohamed
▴ 30
1
vote
2
replies
432
views
Improving the design matrices vignette in RNAseq123
RNAseq123
6 months ago
Lluís Revilla Sancho
▴ 760
0
votes
2
replies
795
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
21 months ago
fatemeh.peimani
• 0
0
votes
0
replies
651
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.8 years ago
rpokhre2
• 0
0
votes
1
reply
963
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
kusum
• 0
0
votes
0
replies
196
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
6 weeks ago
tim.meese
• 0
0
votes
1
reply
1.9k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.0 years ago by
James W. MacDonald
67k • written 2.0 years ago by
Mohamed
▴ 30
0
votes
0
replies
700
views
Plotting a line plot for genes across 4-species
RNAseq123
2.3 years ago
Mohamed
▴ 30
0
votes
3
replies
1.2k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 22 months ago by
Michael Love
42k • written 22 months ago by
irish.prg
• 0
17 results • Page
1 of 1
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Replies
Comment: Volcano plot has many values around zero
by
Michael Love
42k
It's positive over zero or nearly so.
Answer: Volcano plot has many values around zero
by
swbarnes2
★ 1.4k
You've got genes with supposedly have a 32-fold difference, and the adjusted p-values are < 1x10-10? That seems odd.
Comment: Volcano plot has many values around zero
by
mjun
• 0
Why this cluster close to 0 with low p value is so distinctive. Is this common? What does it mean and why? Thanks
Comment: Volcano plot has many values around zero
by
swbarnes2
★ 1.4k
I don't think this is evidence that the dataset is invalid. It's evidence that your experiment is underpowered, and/or your experimental c…
Comment: Differential Expression Analysis with unbalanced batches without replication bet
by
Gordon Smyth
51k
Have you read the totalVI documentation?, which says: > **Important** > We do not recommend using totalVI denoised values in other differ…
Votes
Comment: Weird looking volcano plot
Volcano plot has many values around zero
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
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