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RNAseq123
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291
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
5 months ago
tim.meese
• 0
1
vote
2
replies
503
views
Improving the design matrices vignette in RNAseq123
RNAseq123
10 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
725
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 15 months ago by
ATpoint
★ 4.7k • written 15 months ago by
kaurprab
• 0
0
votes
2
replies
906
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
2.0 years ago
fatemeh.peimani
• 0
0
votes
3
replies
1.3k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
irish.prg
• 0
1
vote
6
replies
5.2k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.2 years ago
afsanarupa1
• 0
2
votes
5
replies
1.4k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 2.2 years ago by
Gordon Smyth
52k • written 2.3 years ago by
Istvan Albert
▴ 50
0
votes
1
reply
2.2k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Mohamed
▴ 30
1
vote
1
reply
1.0k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.5 years ago by
ATpoint
★ 4.7k • written 2.5 years ago by
Mohamed
▴ 30
0
votes
0
replies
765
views
Plotting a line plot for genes across 4-species
RNAseq123
2.6 years ago
Mohamed
▴ 30
2
votes
1
reply
1.4k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.7 years ago by
Gordon Smyth
52k • written 2.7 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.6k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.9 years ago
Alan
• 0
0
votes
1
reply
1.1k
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.6 years ago by
kusum
• 0
1
vote
1
reply
2.0k
views
featureCounts running too long
RNAseq123
updated 13 months ago by
difraiadomenico
• 0 • written 4.0 years ago by
demirkalecy
▴ 10
0
votes
0
replies
718
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
4.1 years ago
rpokhre2
• 0
1
vote
3
replies
5.7k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 4.2 years ago by
mmicky5050
• 0
12
votes
4
replies
5.0k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 6.2 years ago by
Gordon Smyth
52k • written 7.7 years ago by
wd
▴ 30
17 results • Page
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Replies
Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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