0
votes
3
replies
253
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 9 days ago by 65k • written 10 days ago by • 0
3
votes
3
replies
245
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 10 days ago by ★ 4.1k • written 10 days ago by ▴ 10
1
vote
1
reply
138
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 13 days ago by ▴ 40 • written 13 days ago by ★ 1.5k
1
vote
3
replies
234
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 13 days ago by 42k • written 14 days ago by • 0
1
vote
7
replies
338
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
14 days ago • updated 13 days ago pl23 • 0
2
votes
9
replies
404
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 14 days ago by 65k • written 14 days ago by • 0
0
votes
0
replies
130
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
14 days ago • updated 6 days ago glaciya2018 • 0
0
votes
2
replies
215
views
PCA plot suggestions
DESeq2 PCAtools
updated 13 days ago by 42k • written 14 days ago by • 0
0
votes
1
reply
156
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
1
reply
142
views
ATACseq merge peaks
DiffBind
updated 13 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
0
replies
92
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
15 days ago • updated 10 days ago Sara • 0
0
votes
0
replies
87
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
15 days ago Dario Strbenac ★ 1.5k
1
vote
2
replies
165
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
15 days ago • updated 14 days ago ATpoint ★ 4.1k
1
vote
3
replies
221
views
Different Shrunk Log2FC according with reference
DESeq2
updated 15 days ago by 42k • written 15 days ago by ▴ 20
1
vote
4
replies
343
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
15 days ago • updated 13 days ago winwater0928 • 0
2
votes
5
replies
278
views
get BM error
ensembldb
updated 15 days ago by 65k • written 15 days ago by • 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 14 days ago by 65k • written 16 days ago by • 0
1
vote
1
reply
183
views
Citation for edgeR user guide
edgeR
updated 16 days ago by 50k • written 16 days ago by ▴ 30
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 days ago by 42k • written 16 days ago by ▴ 40
1
vote
1
reply
120
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 16 days ago by 65k • written 16 days ago by ▴ 10
0
votes
8
replies
360
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 14 days ago by ★ 1.3k • written 16 days ago by • 0
0
votes
0
replies
76
views
News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
16 days ago info ▴ 10
0
votes
2
replies
257
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
16 days ago • updated 14 days ago shuwangxinze1996 • 0
0
votes
2
replies
173
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 17 days ago by • 0
3
votes
3
replies
233
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
1
vote
4
replies
213
views
minfi::read.metharray.exp
minfiData minfi
updated 15 days ago by ▴ 780 • written 17 days ago by • 0
1
vote
2
replies
194
views
Improving the design matrices vignette in RNAseq123
RNAseq123
17 days ago • updated 3 days ago Lluís Revilla Sancho ▴ 730
0
votes
5
replies
305
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 15 days ago by 65k • written 18 days ago by • 0
2
votes
13
replies
439
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
18 days ago • updated 15 days ago fernanda.backsouza ▴ 10
0
votes
0
replies
85
views
Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
18 days ago vaxahey107 • 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
19 days ago • updated 8 days ago Chris • 0
0
votes
0
replies
100
views
I am trying to detect alternative splicing.
ASpli
19 days ago Sebashish • 0
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 17 days ago by ★ 3.9k • written 20 days ago by ▴ 10
0
votes
1
reply
130
views
FDR via q-value
qvalue
updated 17 days ago by 65k • written 20 days ago by • 0
0
votes
2
replies
221
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
20 days ago • updated 17 days ago catv • 0
0
votes
3
replies
157
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 20 days ago by 65k • written 20 days ago by ▴ 30
1
vote
0
replies
304
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
20 days ago BioinfGuru ▴ 30
0
votes
2
replies
140
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
20 days ago prity6459 • 0
2
votes
2
replies
195
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 20 days ago by 65k • written 21 days ago by • 0
0
votes
4
replies
209
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
21 days ago sropri • 0
1
vote
4
replies
247
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 17 days ago by 65k • written 21 days ago by • 0
0
votes
3
replies
194
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 20 days ago by 50k • written 21 days ago by • 0
0
votes
0
replies
122
views
Warning while loading DEP package
DEP
updated 21 days ago by 3.9k • written 21 days ago by • 0
0
votes
3
replies
177
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by ★ 1.9k • written 21 days ago by • 0
0
votes
1
reply
140
views
rlog transformation
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
1
reply
115
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 days ago by 42k • written 21 days ago by • 0
3
votes
3
replies
238
views
Log-cpm values from limma
limma edgeR RNASeq
updated 3 hours ago by 50k • written 21 days ago by • 0
1
vote
2
replies
224
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
21 days ago Le • 0
1
vote
2
replies
164
views
Error in champ.load(): The following specified files do not exist
ChAMP
22 days ago • updated 21 days ago Sherin • 0
0
votes
1
reply
102
views
Input Question for deseq.r
RSeqAn
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
1,000 results • Page 2 of 20
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.3k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data by Abbey • 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards • All
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Popular Question to Haibo Liu • 0
Popular Question to HS ▴ 10
Locations • All
China, 6 minutes ago
United States, 8 minutes ago
Australia, 9 minutes ago
India, 31 minutes ago
San Diego, 37 minutes ago
Traffic: 479 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