Showing : DESEQ2 • reset
0
votes
1
reply
750
views
DESeq2 - lfcShrink reversing sign for all logFCs - clarification on "contrast" argument?
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
4
replies
1.4k
views
write.table of DESeq2 results broken down by LFC
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 60
1
vote
1
reply
527
views
Differential gene expression analysis
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
4
replies
2.1k
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 80
0
votes
5
replies
1.9k
views
tximeta link to transcriptome
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
6
replies
1.7k
views
Paired t-test with DESeq2
deseq2
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by ▴ 30
0
votes
4
replies
2.4k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
6.1 years ago luciest.rodriguez • 0
0
votes
4
replies
2.5k
views
DESeq2 using many cores despite parallel = FALSE
deseq2 parallel
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
8
votes
18
replies
17k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 4.8 years ago by • 0 • written 6.1 years ago by ▴ 10
2
votes
2
replies
2.1k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
3
votes
6
replies
3.0k
views
Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
6.1 years ago • updated 3.8 years ago hermidalc ▴ 20
3
votes
4
replies
1.2k
views
DESeq2 VS edgeR DEG results different in analysis same data
DESeq2 edgeR
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
2
votes
4
replies
1.1k
views
Combining RSEM Files with dif row # for tximport
tximport DEseq2 RNAseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
6
replies
3.0k
views
Batch effects between different sequencing runs
deseq2 batchcorrection
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by ▴ 60
3
votes
3
replies
1.2k
views
DESeq2 lfcshrink generate 0 svalues
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
3
replies
1.5k
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
6.1 years ago cp1015 • 0
2
votes
5
replies
2.2k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 6.1 years ago by ★ 3.4k • written 6.2 years ago by • 0
4
votes
10
replies
2.2k
views
DeSeq2 Design (A-B)-(C-D)
deseq2 limma
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 30
0
votes
1
reply
1.7k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
3
votes
3
replies
1.4k
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
6
replies
3.2k
views
Extracting VST matrix with batch effects removed
deseq2 batchcorrection
6.1 years ago A ▴ 60
2
votes
1
reply
3.3k
views
How to perform a differential expression analysis from TCGA file EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
cancer limma deseq2
updated 6.1 years ago by ▴ 840 • written 6.1 years ago by ▴ 20
2
votes
6
replies
986
views
Deseq metadata bug on repeat runs with parallel
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
3
replies
699
views
DESeq2 Identical P values in both standard and multi factor design
deseq2 r
6.1 years ago dtlloyd • 0
6
votes
19
replies
5.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 19 months ago by • 0 • written 6.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
DESeq Normalisation, miRNASeq
deseq2 normalization miRNASeq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
5
replies
776
views
Differential expression analyses
normalization deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
4
replies
1.2k
views
DESeq2: Internal reference and multiple comparisons
deseq2
updated 6.2 years ago by • 0 • written 6.2 years ago by • 0
0
votes
4
replies
1.0k
views
non-significant p-values from DESeq2 for some genes, visually the data looks significant
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
vote
3
replies
2.1k
views
delete samples from summarizedExperiment
deseq2
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
3
votes
2
replies
2.7k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
1
vote
8
replies
1.1k
views
high lcfSE for genes with zero counts in the majority of conditions
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq2 very high log2foldchange values
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
2
replies
934
views
rlog() is not working ?
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
4
replies
1.5k
views
DESeq2 - controlling for block vs analysing blocks separately and lfcShrink changes the DE genes drastically
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
0
votes
6
replies
1.1k
views
DESeq2 design for paired samples 'Model matrix not full rank'
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
11
replies
1.9k
views
DEseq2 design for knockdown conditions and treatment
deseq2
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by • 0
1
vote
2
replies
1.5k
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
6
votes
5
replies
1.8k
views
DESeq2 lfcShrink and unshrunk fold changes
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 50
0
votes
1
reply
834
views
51 views DESeq2 RNAseq differential expression analysis
deseq2 likelihood ratio rna seq wald test
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
vote
8
replies
1.1k
views
Responder Vs Non-Responders Paired Comparison DESeq2
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
1
reply
1.5k
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
1
vote
3
replies
4.4k
views
Multi-factor analysis Deseq2
deseq2 contrast LTR
7.1 years ago • updated 6.2 years ago Iryna • 0
1
vote
1
reply
1.1k
views
DESeq2 RNAseq differential expression analysis
deseq2 rnaseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
5
replies
1.4k
views
FPM value and batch correction
deseq2 limma
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
18
replies
4.5k
views
Subset-ing Large DESeqDataSet for data extraction with contrast function
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
3
replies
2.1k
views
Deseq2 post functional annotation for metagenome
deseq2 metagenome mocat
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
2
votes
3
replies
2.0k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
1
reply
669
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
deseq2 RNA-Seq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
1
reply
730
views
rlog in reference level
deseq2
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by ▴ 10
4,839 results • Page 46 of 97
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
United States, 1 hour ago
Pittsburgh, United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 645 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6