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
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
0
votes
9
replies
850
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
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
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
855
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
8 months ago mjd275 • 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
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.5 years ago by ▴ 60
2
votes
9
replies
390
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 11 days ago by • 0
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
4
votes
9
replies
1.3k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 8 months ago by ▴ 10 • written 8 months ago by ▴ 10
6
votes
9
replies
767
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 3 months ago by • 0 • written 3 months ago by • 0
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
1
vote
8
replies
1.3k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 5 weeks ago by ★ 13k • written 10 months ago by ▴ 10
0
votes
8
replies
641
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 10 weeks ago Marianna ▴ 20
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
0
votes
8
replies
1.3k
views
Question about filterByExpr function edgeR
edgeR
8 months ago lucap • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 13 days ago by • 0 • written 7.7 years ago by ▴ 30
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
0
votes
8
replies
712
views
GOslim missing GO term
GO.db GOslim
5 months ago amanda • 0
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 21 months 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
4
votes
8
replies
397
views
Memory errors using read.bismark?
dmrseq bsseq
updated 17 days ago by ▴ 740 • written 25 days 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
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
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
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
0
votes
8
replies
1.1k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray TileDBArray
7 months ago sandmann.t ▴ 70
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
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
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
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
3
votes
8
replies
914
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
0
votes
8
replies
717
views
Deseq2 Results are different using batch design
DESeq2
9 months ago hemantcnaik • 0
2
votes
8
replies
541
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
3
votes
8
replies
524
views
Downloading package mixOmics
mixOmics
10 weeks ago noortje_bloem94 • 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago Habil Zare ▴ 200
0
votes
8
replies
404
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 0
1
vote
8
replies
548
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
11 months ago • updated 10 months ago Ndimensional ▴ 20
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
821
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
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
3
votes
8
replies
515
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
0
votes
8
replies
346
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 days ago by ★ 1.3k • written 13 days ago by • 0
0
votes
8
replies
8.6k
views
Bioconductor version cannot be validated
BiocManager Bioconductor
updated 5 months ago by 690 • written 2.8 years ago by ▴ 10
0
votes
7
replies
1.8k
views
error with champ.load
ChAMP champ methylation
updated 8 months ago by • 0 • written 4.1 years ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
1,744 results • Page 3 of 35
Recent ...
Replies
Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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