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RNAseq123
•
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12
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4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.3 years ago by
Gordon Smyth
50k • written 6.9 years ago by
wd
▴ 30
1
vote
3
replies
4.4k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 3.3 years ago by
mmicky5050
• 0
0
votes
3
replies
817
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 16 months ago by
Michael Love
41k • written 16 months ago by
irish.prg
• 0
2
votes
5
replies
1.0k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Istvan Albert
▴ 50
0
votes
1
reply
811
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
kusum
• 0
1
vote
1
reply
151
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Mohamed
▴ 30
2
votes
1
reply
1.0k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
Mikołaj Mierzejewski
• 0
0
votes
2
replies
540
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
14 months ago
fatemeh.peimani
• 0
1
vote
6
replies
3.2k
views
KEGG enrichment analysis for non model organism
RNAseq123
17 months ago
afsanarupa1
• 0
1
vote
1
reply
331
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
kaurprab
• 0
5
votes
6
replies
2.4k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.0 years ago
Alan
• 0
1
vote
1
reply
1.3k
views
featureCounts running too long
RNAseq123
updated 12 weeks ago by
difraiadomenico
• 0 • written 3.1 years ago by
demirkalecy
▴ 10
0
votes
0
replies
547
views
Plotting a line plot for genes across 4-species
RNAseq123
21 months ago
Mohamed
▴ 30
0
votes
0
replies
503
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.2 years ago
rpokhre2
• 0
1
vote
1
reply
708
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 19 months ago by
ATpoint
★ 4.1k • written 19 months ago by
Mohamed
▴ 30
16 results • Page
1 of 1
Recent ...
Replies
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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