Showing : DifferentialExpression • reset
0
votes
3
replies
128
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 5 days ago by 42k • written 6 days ago by • 0
1
vote
3
replies
256
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 5 days ago by 50k • written 6 days ago by • 0
0
votes
1
reply
183
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
2
votes
7
replies
417
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
12 days ago • updated 9 days ago sajadahmad41454 • 0
0
votes
3
replies
228
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
0
votes
3
replies
282
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 days ago by 65k • written 21 days ago by • 0
0
votes
2
replies
248
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
5
votes
6
replies
462
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
1
vote
3
replies
284
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
2
replies
184
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
1
vote
2
replies
251
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
8 weeks ago • updated 7 weeks ago Chanderkant Chaudhary • 0
5
votes
3
replies
743
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
0
votes
2
replies
305
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
2
replies
349
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
1
vote
3
replies
443
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
votes
4
replies
520
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
votes
4
replies
328
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
0
votes
0
replies
243
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
2
votes
1
reply
321
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
3
votes
2
replies
322
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
4
votes
3
replies
385
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
3
replies
392
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
1
reply
237
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by ▴ 20
0
votes
2
replies
329
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by • 0
5
votes
6
replies
609
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago • updated 3 months ago Shaimaa Gamal • 0
4
votes
6
replies
653
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
331
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
1
vote
3
replies
615
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 5 months ago by • 0
0
votes
5
replies
646
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
votes
3
replies
440
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
1
reply
420
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
2
votes
4
replies
552
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 5 months ago by • 0
0
votes
2
replies
380
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
1
vote
2
replies
464
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
1
reply
372
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 6 months ago by 42k • written 6 months ago by ▴ 10
1
vote
4
replies
589
views
rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 6 months ago by 42k • written 6 months ago by ▴ 60
0
votes
8
replies
845
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
0
votes
0
replies
390
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
7 months ago nromerov • 0
2
votes
6
replies
802
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
2
votes
4
replies
728
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
votes
1
reply
441
views
''Model_Matrix'' error
DifferentialExpression limma
updated 7 months ago by 50k • written 8 months ago by • 0
3
votes
3
replies
596
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
3
replies
470
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
2
replies
536
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
0
votes
1
reply
516
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 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
414
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 8 months ago by 65k • written 8 months ago by • 0
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
1
vote
3
replies
594
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
0
votes
0
replies
451
views
DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
6
replies
812
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 50k • written 10 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
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 65k
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 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards • All
Popular Question to landenshanie ▴ 40
Popular Question to minardsmitha ▴ 10
Teacher to Vincent J. Carey, Jr. 6.7k
Popular Question to Mike • -60
Popular Question to shepherl 3.9k
Locations • All
Sweden, 2 minutes ago
United States, 18 minutes ago
Germany, 19 minutes ago
United States, 20 minutes ago
Poland, 22 minutes ago
Traffic: 681 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