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
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 6.6 years ago by ▴ 60
1
vote
9
replies
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.2 years ago by • 0
0
votes
9
replies
592
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
9 months ago 15753563659 ▴ 50
2
votes
9
replies
1.8k
views
How to load fasta file with openPrimeR?
openPrimeR
written 3.3 years ago by • 0
1
vote
9
replies
3.0k
views
DEGreport installation help
DEGreport
updated 8 months ago by 65k • written 19 months ago by ▴ 20
4
votes
9
replies
491
views
Memory errors using read.bismark?
dmrseq bsseq
5 weeks ago • updated 11 days ago Juan Higareda • 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
4
votes
9
replies
249
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
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 9 months ago by • 0 • written 6.5 years ago by ▴ 10
0
votes
9
replies
3.2k
views
clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.2 years ago by • 0
1
vote
9
replies
910
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
2
votes
9
replies
427
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 23 days ago by 65k • written 23 days ago by • 0
0
votes
8
replies
497
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 4 days ago by ▴ 30 • written 5 days ago by • 0
3
votes
8
replies
542
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
0
votes
8
replies
8.7k
views
Bioconductor version cannot be validated
BiocManager Bioconductor
updated 5 months ago by 700 • written 2.8 years ago by ▴ 10
0
votes
8
replies
387
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 24 days ago by ★ 1.4k • written 25 days ago by • 0
0
votes
8
replies
456
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
10 weeks ago michelafrancesconi8 • 0
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 5 months ago by • 0 • written 12 months ago by ▴ 10
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
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib rhdf5
3.2 years ago • updated 9 months ago Thomas Sandmann ▴ 90
1
vote
8
replies
1.3k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 6 weeks ago by ★ 13k • written 10 months ago by ▴ 10
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
562
views
Downloading package mixOmics
mixOmics
12 weeks ago noortje_bloem94 • 0
2
votes
8
replies
1.8k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 21 months ago by ▴ 10
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 6 months ago by • 0 • written 14 months ago by • 0
0
votes
8
replies
735
views
Deseq2 Results are different using batch design
DESeq2
10 months ago • updated 9 months ago hemantcnaik • 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 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
1.1k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray TileDBArray
8 months ago sandmann.t ▴ 70
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
1
vote
8
replies
581
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
8
replies
683
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
2
votes
8
replies
1.3k
views
Reading GFF file and pre-processing, run iinfer_syntenet(), input and output
syntenet
updated 4 months ago by • 0 • written 16 months ago by • 0
0
votes
8
replies
1.4k
views
Question about filterByExpr function edgeR
edgeR
9 months ago lucap • 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
12 months ago • updated 11 months ago Habil Zare ▴ 200
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 10 months ago by ▴ 180 • written 17 months ago by ▴ 30
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 25 days ago by • 0 • written 7.8 years ago by ▴ 30
0
votes
8
replies
844
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
10
votes
8
replies
4.0k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by • 0 • written 6.9 years ago by ▴ 30
3
votes
8
replies
933
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
1.7k
views
flowset/ncdfFlowset replace keywords doesn't work right
ncdfFlow flowCore
updated 8 months ago by • 0 • written 3.6 years ago by ▴ 30
1
vote
8
replies
1.6k
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 11 months ago by • 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 10
2
votes
8
replies
564
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
8
votes
8
replies
9.9k
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
0
votes
8
replies
756
views
GOslim missing GO term
GO.db GOslim
5 months ago amanda • 0
0
votes
7
replies
689
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 11 weeks ago by ▴ 10 • written 5 months ago by • 0
4
votes
7
replies
1.1k
views
Fishpond/Swish Interaction Test Error
fishpond swish
11 months ago Miguel ▴ 20
1,000 results • Page 3 of 20
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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