Showing : differentialexpression • reset
0
votes
2
replies
175
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 8 days ago by 41k • written 12 days ago by ▴ 30
5
votes
6
replies
361
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 days ago by ★ 4.0k • written 8 days ago by ▴ 30
1
vote
3
replies
211
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 12 days ago by 65k • written 12 days ago by • 0
0
votes
2
replies
127
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 12 days ago by 65k • written 12 days ago by • 0
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
27 days ago • updated 21 days ago Chanderkant Chaudhary • 0
5
votes
3
replies
660
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 21 days ago by 50k • written 28 days ago by ▴ 50
0
votes
2
replies
243
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
2
replies
289
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
3
replies
350
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 10 weeks ago by • 0
3
votes
4
replies
364
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by ▴ 50
0
votes
4
replies
260
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago • updated 6 weeks ago mperalc • 0
0
votes
0
replies
186
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
2
votes
1
reply
272
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 8 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
3
votes
2
replies
258
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago • updated 9 weeks ago Shaimaa Gamal • 0
4
votes
3
replies
312
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
votes
3
replies
327
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
1
reply
200
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 weeks ago by 41k • written 10 weeks ago by ▴ 20
0
votes
2
replies
266
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 11 weeks ago by 41k • written 11 weeks ago by • 0
5
votes
6
replies
514
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 weeks ago Shaimaa Gamal • 0
4
votes
6
replies
537
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
votes
1
reply
245
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
3
replies
557
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 3 months ago by • 0
0
votes
5
replies
584
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 11 weeks ago Lucy ▴ 60
0
votes
3
replies
404
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
vote
1
reply
375
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
votes
4
replies
473
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
0
votes
2
replies
314
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
vote
2
replies
371
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
1
reply
317
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by 41k • written 5 months ago by ▴ 10
1
vote
4
replies
522
views
rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 5 months ago by 41k • written 5 months ago by ▴ 60
0
votes
8
replies
788
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
5 months ago Luca • 0
0
votes
0
replies
337
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
2
votes
6
replies
744
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
2
votes
4
replies
640
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
6 months ago Shihui • 0
0
votes
1
reply
393
views
''Model_Matrix'' error
DifferentialExpression limma
updated 6 months ago by 50k • written 6 months ago by • 0
3
votes
3
replies
555
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
3
replies
438
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
2
replies
484
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
0
votes
1
reply
486
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
1
reply
362
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 7 months ago by 65k • written 7 months ago by • 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 20
1
vote
3
replies
532
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by ▴ 10
0
votes
0
replies
426
views
DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
6
replies
747
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
2
replies
658
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
1
vote
1
reply
512
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
8
replies
1.5k
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 10 months ago by • 0
0
votes
3
replies
625
views
limma paired design
DifferentialExpression limma
updated 9 months ago by 65k • written 10 months ago by • 0
0
votes
1
reply
488
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
1
vote
0
replies
451
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 10 months ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
United States, 13 minutes ago
United States, 18 minutes ago
France, 20 minutes ago
United States, 27 minutes ago
WEHI, Melbourne, Australia, 42 minutes ago
Traffic: 524 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