Showing : drimseq • reset
1
vote
1
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370
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
5 months ago NiKo ▴ 10
0
votes
0
replies
379
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
12 months ago Luca • 0
0
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3
replies
663
views
DRIMseq error for paired sample analysis
DRIMSeq
12 months ago Luca • 0
2
votes
2
replies
677
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU DRIMSeq
21 months ago wangziwei0010 ▴ 10
0
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4
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1.4k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 23 months ago by ▴ 90 • written 24 months ago by • 0
0
votes
5
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1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
3
votes
4
replies
1.1k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
2.8 years ago sbcn ▴ 80
0
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0
replies
861
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.1 years ago jbono ▴ 10
0
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2
replies
985
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.1 years ago Gaia • 0
0
votes
5
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1.4k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
1
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1
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794
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq tuQTL
updated 3.7 years ago by ▴ 90 • written 3.8 years ago by • 0
0
votes
5
replies
1.1k
views
DRIMSeq with technical replicates
DRIMSeq R DTU technical replicates deseq2
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by • 0
1
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1
reply
810
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport DEXSeq-DTU DRIMSeq
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
0
votes
0
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653
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
3.9 years ago alexis.weinreb • 0
0
votes
11
replies
1.5k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
5.1 years ago • updated 5.0 years ago saddamhusain77 • 0
0
votes
1
reply
825
views
stageR with input from DRIMSeq
DRIMSeq stageR
updated 5.1 years ago by ▴ 180 • written 5.1 years ago by • 0
1
vote
2
replies
1.4k
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 5.2 years ago by ▴ 90 • written 5.2 years ago by ▴ 30
0
votes
4
replies
1.4k
views
DRIMSeq continious variable in design matrix - Error during precision estimation
DRIMSeq dmPrecision
updated 14 months ago by • 0 • written 5.2 years ago by ▴ 60
2
votes
4
replies
1.6k
views
stageR: Error in stageWiseAdjustment
stageR rnaseqDTU DRIMSeq DEXSeq
5.2 years ago d-joester ▴ 20
2
votes
2
replies
1.1k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU DRIMSeq rnaseqDTU
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 60
0
votes
3
replies
1.0k
views
Post-hoc filtering on the standard deviation in proportions
drimseq rnaseqdtu stager
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
1
vote
1
reply
761
views
Calling a package specific function in a for loop
drimseq swimming downstream for loop sapply
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
4
votes
3
replies
1.4k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 5.6 years ago by ▴ 90 • written 5.6 years ago by • 0
2
votes
9
replies
1.7k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq stageR dtu salmon rna seq
updated 5.8 years ago by ▴ 180 • written 5.8 years ago by ▴ 60
1
vote
1
reply
1.3k
views
DrimSeq: installation versions
drimseq DTU
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq splicing differential isoform usage
updated 7.2 years ago by ▴ 90 • written 7.2 years ago by ▴ 20
26 results • Page 1 of 1
Recent ...
Replies
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…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
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?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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