2
votes
2
replies
1.8k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
21 months ago Eva ▴ 10
0
votes
4
replies
1.1k
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
21 months ago • updated 20 months ago Efra • 0
1
vote
1
reply
716
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
1
reply
452
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
1
reply
1.6k
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
3
votes
9
replies
8.2k
views
enrichGOgradient color change
clusterProfiler
updated 11 months ago by • 0 • written 2.1 years ago by • 0
1
vote
5
replies
1.4k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
21 months ago Gerhard Thallinger ▴ 180
5
votes
7
replies
1.6k
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 20 months ago by 53k • written 21 months ago by • 0
0
votes
2
replies
886
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
1
reply
1.4k
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium genom linka GenomicDistributionsData
updated 21 months ago by 68k • written 21 months ago by ▴ 10
2
votes
2
replies
783
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
21 months ago feather-W • 0
0
votes
1
reply
696
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 21 months ago by 53k • written 21 months ago by ▴ 180
2
votes
2
replies
963
views
between lane normalization upper quantile
EDASeq edgeR
21 months ago elesofi • 0
2
votes
3
replies
3.6k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 21 months ago by ★ 5.0k • written 3.7 years ago by ▴ 20
0
votes
1
reply
700
views
problem with ClusterRepro function
WGCNA
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
2
replies
1.2k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
4
replies
888
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
2
votes
2
replies
863
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
21 months ago Sabiha ▴ 20
0
votes
10
replies
1.7k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 21 months ago by • 0
0
votes
2
replies
940
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
21 months ago Sam ▴ 10
0
votes
2
replies
3.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
21 months ago kcarey • 0
1
vote
1
reply
602
views
i'm not getting any differentially expressed genes.
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
2
votes
1
reply
826
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
1
reply
783
views
Exact same results in Diffbind with different normalization methods
DiffBind
21 months ago red_bricks ▴ 60
0
votes
0
replies
549
views
FELLA plotGraph function won't change the legend
FELLA
21 months ago yuhang • 0
0
votes
0
replies
479
views
medips-output
ngsReports MEDIPS
21 months ago Researcher ▴ 10
1
vote
1
reply
786
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas db0
updated 7 weeks ago by • 0 • written 21 months ago by ▴ 10
0
votes
1
reply
612
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 21 months ago by ▴ 40 • written 22 months ago by • 0
0
votes
1
reply
696
views
question about data processing for syntenet
syntenet
updated 21 months ago by ▴ 40 • written 23 months ago by • 0
0
votes
4
replies
779
views
Error in classify_gene_pairs
syntenet doubletrouble
21 months ago hfyuan2016 • 0
2
votes
1
reply
752
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 21 months ago by 68k • written 21 months ago by ▴ 180
0
votes
0
replies
418
views
The graphical interface of FELLA doesn't work
FELLA
21 months ago yuhang • 0
0
votes
0
replies
500
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
21 months ago jean-christophe.helbling • 0
1
vote
1
reply
525
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
votes
2
replies
965
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 months ago Viktor Thiel • 0
0
votes
0
replies
648
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
21 months ago Henry • 0
0
votes
1
reply
1.2k
views
Rcpp compilation error
Release Rcpp
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 40
0
votes
1
reply
805
views
Rain error: invalid annotation of time points
rain
updated 10 months ago by • 0 • written 21 months ago by • 0
0
votes
0
replies
785
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
21 months ago Felix • 0
0
votes
1
reply
853
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
vote
2
replies
785
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
21 months ago thomas • 0
1
vote
1
reply
622
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
8
replies
1.6k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
21 months ago michelafrancesconi8 • 0
0
votes
1
reply
674
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
1
reply
723
views
News: Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
written 21 months ago by • 0
2
votes
6
replies
1.6k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
21 months ago • updated 20 months ago Lily Cheang ▴ 10
3
votes
8
replies
1.4k
views
Constrast for Time Course Experiments using Limma
limma
21 months ago dl17032000 • 0
1
vote
4
replies
921
views
DESeq2 Replicates
DESeq2 RNASeq
21 months ago kcarey • 0
2
votes
6
replies
1.0k
views
Factor vs Character in design
DESeq2
21 months ago James Aiden • 0
46,692 results • Page 29 of 934
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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