0
votes
9
replies
1.4k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
8 months ago 15753563659 ▴ 50
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.5 years ago by ▴ 10
0
votes
9
replies
560
views
limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.2 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
2
votes
9
replies
357
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 days ago by 65k • written 9 days ago by • 0
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
6
votes
9
replies
761
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 3 months ago by • 0 • written 3 months ago by • 0
4
votes
9
replies
4.4k
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
0
votes
9
replies
846
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
0
votes
8
replies
820
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago • updated 5 months ago Luca • 0
0
votes
8
replies
1.1k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray TileDBArray
7 months ago sandmann.t ▴ 70
0
votes
8
replies
1.3k
views
Question about filterByExpr function edgeR
edgeR
8 months ago lucap • 0
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
0
votes
8
replies
714
views
Deseq2 Results are different using batch design
DESeq2
9 months ago hemantcnaik • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 11 days ago by • 0 • written 7.7 years ago by ▴ 30
0
votes
8
replies
634
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
11 weeks ago • updated 10 weeks ago Marianna ▴ 20
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 4 weeks ago by ★ 13k • written 10 months ago by ▴ 10
1
vote
8
replies
1.5k
views
News: Final List of Deprecated Package Bioc 3.9
deprecation release software experimentData News
written 5.1 years ago by 3.9k
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 20 months ago by ▴ 10
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
0
votes
8
replies
1.7k
views
flowset/ncdfFlowset replace keywords doesn't work right
ncdfFlow flowCore
updated 7 months ago by • 0 • written 3.6 years ago by ▴ 30
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago Habil Zare ▴ 200
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib rhdf5
3.2 years ago • updated 8 months ago Thomas Sandmann ▴ 90
0
votes
8
replies
708
views
GOslim missing GO term
GO.db GOslim
5 months ago amanda • 0
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago Luis • 0
3
votes
8
replies
517
views
Downloading package mixOmics
mixOmics
10 weeks ago noortje_bloem94 • 0
0
votes
8
replies
399
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 0
1
vote
8
replies
544
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 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
10 months ago Ndimensional ▴ 20
2
votes
8
replies
1.3k
views
Reading GFF file and pre-processing, run iinfer_syntenet(), input and output
syntenet
updated 3 months ago by • 0 • written 16 months ago by • 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
4
votes
8
replies
389
views
Memory errors using read.bismark?
dmrseq bsseq
updated 15 days ago by ▴ 740 • written 23 days ago by • 0
3
votes
8
replies
505
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
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 11 months ago by 50k • written 17 months ago by ▴ 20
8
votes
8
replies
9.8k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 7 months ago by • 0 • written 4.8 years ago by ▴ 40
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by • 0 • written 6.8 years ago by ▴ 30
0
votes
8
replies
338
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 9 days ago by ★ 1.3k • written 10 days 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
2
votes
8
replies
526
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 14 months ago by • 0
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by ▴ 180 • written 17 months ago by ▴ 30
0
votes
8
replies
8.6k
views
Bioconductor version cannot be validated
BiocManager Bioconductor
updated 5 months ago by 690 • written 2.7 years ago by ▴ 10
3
votes
8
replies
909
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
0
votes
7
replies
308
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
17 days ago • updated 11 days ago hortense96 • 0
1
vote
7
replies
835
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 6 months ago by • 0
1,743 results • Page 3 of 35
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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