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RNASeq123
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45
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Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago
Lluís Revilla Sancho
▴ 730
1
vote
1
reply
320
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
kaurprab
• 0
0
votes
2
replies
524
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
14 months ago
fatemeh.peimani
• 0
0
votes
3
replies
802
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
1
vote
6
replies
3.1k
views
KEGG enrichment analysis for non model organism
RNAseq123
16 months ago
afsanarupa1
• 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 16 months ago by
Gordon Smyth
50k • written 17 months ago by
Istvan Albert
▴ 50
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 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Mohamed
▴ 30
1
vote
1
reply
694
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
Mohamed
▴ 30
0
votes
0
replies
542
views
Plotting a line plot for genes across 4-species
RNAseq123
21 months ago
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
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
0
votes
1
reply
805
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
kusum
• 0
1
vote
1
reply
1.3k
views
featureCounts running too long
RNAseq123
updated 11 weeks ago by
difraiadomenico
• 0 • written 3.1 years ago by
demirkalecy
▴ 10
0
votes
0
replies
501
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.2 years ago
rpokhre2
• 0
1
vote
3
replies
4.4k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 3.3 years ago by
mmicky5050
• 0
12
votes
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
16 results • Page
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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Gordon Smyth
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