Showing : DEseq2 • reset
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.1 years ago by ▴ 40
25
votes
7
replies
10k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by • 0 • written 8.3 years ago by ▴ 60
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 8 weeks ago by 41k • written 7.8 years ago by ▴ 30
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 20 hours ago by • 0 • written 8.8 years ago by ▴ 30
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
8
votes
12
replies
2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 11 months ago by ▴ 90
8
votes
8
replies
9.7k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 6 months ago by • 0 • written 4.7 years ago by ▴ 40
8
votes
15
replies
1.4k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago • updated 7 months ago IUH • 0
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 11 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
7
votes
4
replies
2.7k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 3 months ago by • 0 • written 6.1 years ago by ▴ 20
7
votes
3
replies
851
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 9 months ago by 41k • written 9 months ago by ▴ 20
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 5 weeks ago by • 0 • written 3.1 years ago by ▴ 40
6
votes
5
replies
4.1k
views
DESeq2: Extremely low pvalues
deseq2
updated 9 months ago by 65k • written 7.7 years ago by ▴ 20
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 8 months ago by • 0 • written 9.2 years ago by ▴ 40
5
votes
2
replies
845
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
8 months ago Alessia ▴ 40
5
votes
7
replies
1.0k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
5
votes
15
replies
4.9k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
5
votes
18
replies
7.4k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.2 years ago by • 0
5
votes
12
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by • 0 • written 4.6 years ago by ▴ 10
4
votes
6
replies
2.2k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 11 months ago by 41k • written 12 months ago by • 0
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 5 weeks ago by • 0 • written 12 months ago by ▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 10 months ago by 50k • written 16 months ago by ▴ 20
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 6 months ago by 41k • written 7 months ago by • 0
4
votes
7
replies
829
views
weird volcano plot
DESeq2
updated 6 weeks ago by • 0 • written 5 months ago by ▴ 10
4
votes
7
replies
665
views
DESeq2 unable to handle large count values
DESeq2
updated 4 weeks ago by 41k • written 5 months ago by • 0
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 0
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
8 months ago Luca • 0
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
3
votes
3
replies
960
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 16 months ago by • 0
3
votes
6
replies
814
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
6
replies
2.7k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 8 weeks ago by • 0 • written 5.2 years ago by ▴ 50
3
votes
5
replies
834
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
3
votes
3
replies
532
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by • 0 • written 5.6 years ago by • 0
3
votes
2
replies
657
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
3
votes
5
replies
585
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
votes
2
replies
1.0k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
3
votes
1
reply
602
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
4
replies
839
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
3
votes
3
replies
930
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
3
votes
12
replies
2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by • 0
3
votes
2
replies
189
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
24 days ago Anita ▴ 10
3
votes
2
replies
296
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 10 weeks ago by ▴ 30 • written 10 weeks ago by • 0
3
votes
2
replies
539
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
3
votes
16
replies
2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 12 weeks ago by 3.8k • written 2.8 years ago by ▴ 10
3
votes
7
replies
847
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
7 months ago casco ▴ 10
50 results • Page 1 of 1
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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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