Showing : variancePartition • reset
2
votes
9
replies
743
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 9 weeks ago by 51k • written 10 weeks ago by • 0
1
vote
2
replies
500
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 months ago Le • 0
1
vote
4
replies
1.3k
views
BiocParallel serialization errors on Windows
variancePartition BiocParallel
10 months ago hayleyw • 0
1
vote
7
replies
1.2k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 11 months ago by 51k • written 13 months ago by • 0
0
votes
9
replies
1.3k
views
How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
14 months ago hayleyw • 0
1
vote
5
replies
2.0k
views
How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
19 months ago • updated 18 months ago Weiqian ▴ 10
1
vote
4
replies
945
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
20 months ago DH • 0
0
votes
5
replies
1.3k
views
Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 20 months ago by 51k • written 20 months ago by • 0
0
votes
0
replies
576
views
Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.2 years ago Jonathan • 0
1
vote
1
reply
1.5k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 3.3 years ago by 51k • written 3.3 years ago by • 0
1
vote
3
replies
1.5k
views
limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.4 years ago by 51k • written 3.4 years ago by ▴ 30
1
vote
0
replies
971
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
3.5 years ago Junghoon ▴ 10
0
votes
1
reply
1.3k
views
Error while running variancePartition::dream()
variancePartition limma BiocParallel
3.5 years ago Junghoon ▴ 10
0
votes
1
reply
1.3k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
3.5 years ago • updated 3.4 years ago Junghoon ▴ 10
9
votes
11
replies
2.9k
views
dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 5.1 years ago by 51k • written 5.1 years ago by ▴ 20
3
votes
8
replies
1.9k
views
Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.1 years ago by ▴ 160 • written 5.2 years ago by • 0
4
votes
3
replies
2.2k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.1 years ago by ▴ 160 • written 5.4 years ago by ▴ 50
17 results • Page 1 of 1
Recent ...
Replies
Comment: Problem at champ.load by icecreamlover • 0
Hello! Were you able to figure this out? I am running into the same error!
Comment: ChAMP - obtaining beta values using EPICv2 annotation by icecreamlover • 0
Hello, Were you able to fix the error? I used the same document and I am running into the same error. I am curious if you have any feedba…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
Can this please be revisited and corrected ASAP? I'm encountering the same issue, using a slightly more modern version of R (4.1.0). It s…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Votes
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Awards • All
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Gordon Smyth 51k
Popular Question to shepherl 4.1k
Supporter to Paul Harrison ▴ 100
Popular Question to Mikhail Dozmorov ▴ 30
Locations • All
United States, 7 minutes ago
France, 12 minutes ago
United States, 35 minutes ago
Denmark, 40 minutes ago
San Diego, 41 minutes ago
Traffic: 763 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