3
votes
3
replies
976
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago amnahsiddiqa ▴ 10
3
votes
8
replies
561
views
Downloading package mixOmics
mixOmics
12 weeks ago noortje_bloem94 • 0
3
votes
1
reply
147
views
How to save the DEXSeq results
DEXSeq
updated 11 days ago by 42k • written 11 days ago by • 0
3
votes
5
replies
908
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
3
votes
4
replies
892
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.1k • written 6.4 years ago by • 0
3
votes
2
replies
464
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
3
votes
5
replies
667
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
votes
6
replies
716
views
Methylation data analysis
MethylationArrayData methylationArrayAnalysis
6 months ago aldea85 • 0
3
votes
5
replies
1.7k
views
Error: 'IdClusters'
DECIPHER
updated 11 months ago by ▴ 10 • written 15 months ago by • 0
3
votes
2
replies
581
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
3
votes
1
reply
440
views
NPARC package y-variable
NPARC NPA
updated 8 months ago by ▴ 20 • written 8 months ago by • 0
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
votes
3
replies
9.5k
views
How to find rsID with biomaRt in R
biomaRt
updated 3 months ago by 65k • written 3.2 years ago by ▴ 10
3
votes
7
replies
1.9k
views
Installing densvis on a Singularity container
densvis docker
updated 11 months ago by ▴ 160 • written 12 months ago by 65k
3
votes
5
replies
891
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
8
replies
930
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
3
votes
6
replies
23k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 4 months ago by • 0 • written 5.7 years ago by • 0
3
votes
2
replies
688
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
3
replies
714
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
6
replies
2.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 19 months ago by ▴ 10
3
votes
5
replies
2.2k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 12 weeks ago by • 0 • written 3.4 years ago by • 0
3
votes
2
replies
496
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
3
votes
5
replies
924
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 4 months ago by ▴ 30 • written 18 months ago by • 0
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 3 months ago by ★ 4.0k • written 3.3 years ago by • 0
3
votes
10
replies
2.8k
views
error in package GenVisR while installing
GenVisR GenVis
updated 6 months ago by ▴ 30 • written 22 months ago by • 0
3
votes
6
replies
860
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts rsubread
updated 11 months ago by • 0 • written 9.0 years ago by ▴ 140
3
votes
4
replies
260
views
Help with error using camera() in limma
CAMERA limma
17 days ago Chris ▴ 10
3
votes
4
replies
505
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 9 days ago by ★ 6.5k • written 12 days ago by • 0
3
votes
4
replies
506
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
3
votes
2
replies
478
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
5 months ago kyj2226 • 0
3
votes
5
replies
288
views
Help with running egsea()
EGSEA
11 days ago • updated 10 days ago Chris ▴ 10
3
votes
18
replies
3.0k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 4 weeks ago shepherl 3.9k
3
votes
2
replies
234
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
7 weeks ago Anita ▴ 10
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
votes
2
replies
407
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 3 months ago by ▴ 30 • written 3 months ago by • 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by 42k • written 24 days ago by ▴ 40
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by • 0 • written 5.3 years ago by • 0
3
votes
3
replies
454
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 7 weeks ago by ▴ 160 • written 7 weeks ago by • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
3
votes
16
replies
2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.9k • written 2.9 years ago by ▴ 10
3
votes
6
replies
305
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
3
votes
1
reply
1.4k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 9 months ago by 65k • written 9 months ago by ▴ 10
3
votes
1
reply
327
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
4
replies
696
views
Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
MicroRNAArrayData GSE97562 pd.hugene.1.0.st.v1 Annotation
updated 10 months ago by 65k • written 10 months ago by • 0
3
votes
12
replies
2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 19 months ago by • 0
3
votes
7
replies
882
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
1,738 results • Page 4 of 35
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That would probably make the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
United States, 5 minutes ago
The city by the bay, 56 minutes ago
Poland, 1 hour ago
Melbourne, Australia, 2 hours ago
Ireland, 2 hours ago
Traffic: 449 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