Showing : DESEq2 • reset
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 12 weeks ago by 42k • written 7.9 years ago by ▴ 30
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.2 years ago by ▴ 40
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 20 days ago by • 0 • written 4.6 years ago by ▴ 10
5
votes
18
replies
7.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 5 months ago by • 0 • written 2.3 years ago by • 0
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.6 years ago by • 0
3
votes
16
replies
2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.9k • written 2.9 years ago by ▴ 10
1
vote
15
replies
8.3k
views
Exporting DESeq2 filtered results
DESeq2
updated 7 months ago by 66k • written 3.2 years ago by ▴ 10
5
votes
15
replies
5.1k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 11 months ago by 66k • written 6.9 years ago by ▴ 10
8
votes
15
replies
1.6k
views
PCA percent variance DESeq2
PCA DESeq2
9 months ago • updated 8 months ago IUH • 0
4
votes
13
replies
1.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
0
votes
13
replies
733
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 11 weeks ago by 42k • written 12 weeks ago by • 0
1
vote
13
replies
958
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 4 months ago by ★ 3.9k • written 5 months ago by ▴ 10
2
votes
12
replies
1.4k
views
P-value inflation?
DESeq2
updated 8 months ago by 66k • written 9 months ago by ▴ 10
1
vote
12
replies
2.8k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 7 months ago by ★ 1.5k • written 22 months ago by • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 4 weeks ago by • 0 • written 8.9 years ago by ▴ 30
1
vote
12
replies
1.1k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
12 weeks ago • updated 11 weeks ago paria.alipour • 0
3
votes
12
replies
2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 19 months ago by • 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
6
votes
11
replies
4.1k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 10 weeks ago by • 0 • written 3.2 years ago by ▴ 40
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 9 months ago by • 0 • written 9.3 years ago by ▴ 40
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 10 months ago by 66k • written 10 months ago by • 0
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago rohitsatyam102 ▴ 20
2
votes
10
replies
3.3k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 7 months ago by 42k • written 5.8 years ago by ▴ 20
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
0
votes
9
replies
1.5k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 7 months ago by ▴ 10 • written 22 months ago by ▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
4
votes
9
replies
287
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
9
replies
867
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
9 months ago • updated 8 months ago mjd275 • 0
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 12 months ago by • 0 • written 6.9 years ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
0
votes
9
replies
1.5k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 11 months ago by 42k • written 11 months ago by ▴ 10
2
votes
9
replies
430
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 25 days ago by 66k • written 26 days ago by • 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
10 months ago Luca • 0
1
vote
9
replies
914
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
8
votes
8
replies
9.9k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 8 months ago by • 0 • written 4.8 years ago by ▴ 40
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 12 months ago by 50k • written 17 months ago by ▴ 20
0
votes
8
replies
461
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
10 weeks ago michelafrancesconi8 • 0
0
votes
8
replies
846
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
0
votes
8
replies
740
views
Deseq2 Results are different using batch design
DESeq2
10 months ago hemantcnaik • 0
0
votes
8
replies
398
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 26 days ago by ★ 1.4k • written 27 days ago by • 0
1
vote
8
replies
1.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 11 months ago by • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
0
votes
8
replies
530
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 6 days ago by ▴ 30 • written 7 days ago by • 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 10
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
1
vote
8
replies
1.3k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 7 weeks ago by ★ 13k • written 10 months ago by ▴ 10
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
0
votes
7
replies
454
views
DESeq filtering specific to contrasts
DESeq2
updated 4 weeks ago by 42k • written 3 months ago by • 0
0
votes
7
replies
464
views
DESeq2 filtering vs edgeR filtering
DESeq2
9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
4
votes
7
replies
909
views
weird volcano plot
DESeq2
updated 10 weeks ago by • 0 • written 6 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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