1
vote
3
replies
40
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
1 hour ago • updated 6 minutes ago Alexandre • 0
0
votes
0
replies
20
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
6 hours ago glaciya2018 • 0
0
votes
1
reply
28
views
PCA plot suggestions
DESeq2 PCAtools
updated 16 minutes ago by • 0 • written 10 hours ago by • 0
0
votes
1
reply
70
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 17 hours ago by 41k • written 21 hours ago by • 0
0
votes
0
replies
17
views
ATACseq merge peaks
DiffBind
21 hours ago Shloka • 0
0
votes
0
replies
16
views
Differential splicing from SGSeq analysis
DEXSeq SGSeq
23 hours ago Sara • 0
0
votes
0
replies
26
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
1 day ago Dario Strbenac ★ 1.5k
1
vote
2
replies
76
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
1 day ago • updated 6 hours ago ATpoint ★ 4.0k
1
vote
3
replies
84
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 20
0
votes
3
replies
102
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 1 hour ago by 65k • written 1 day ago by • 0
2
votes
5
replies
139
views
get BM error
ensembldb
updated 22 hours ago by 65k • written 1 day ago by • 0
2
votes
3
replies
101
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 1 day ago by 65k • written 1 day ago by • 0
1
vote
1
reply
70
views
Citation for edgeR user guide
edgeR
updated 1 day ago by 50k • written 1 day ago by ▴ 30
3
votes
1
reply
172
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 40
1
vote
1
reply
55
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 1 day ago by 65k • written 1 day ago by ▴ 10
0
votes
8
replies
219
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 9 hours ago by ★ 1.3k • written 1 day ago by • 0
0
votes
0
replies
25
views
News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
1 day ago info ▴ 10
0
votes
2
replies
106
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
2 days ago • updated 8 hours ago shuwangxinze1996 • 0
0
votes
1
reply
87
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 2 days ago by 50k • written 2 days ago by • 0
3
votes
3
replies
156
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
1
vote
4
replies
129
views
minfi::read.metharray.exp
minfiData minfi
updated 1 day ago by ▴ 780 • written 2 days ago by • 0
0
votes
0
replies
41
views
Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago Lluís Revilla Sancho ▴ 730
0
votes
5
replies
208
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 1 day ago by 65k • written 3 days ago by • 0
1
vote
13
replies
245
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
3 days ago • updated 17 hours ago fernanda.backsouza ▴ 10
0
votes
0
replies
40
views
Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
4 days ago vaxahey107 • 0
12
votes
12
replies
761
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by ★ 3.3k • written 5 days ago by • 0
0
votes
0
replies
61
views
I am trying to detect alternative splicing.
ASpli
5 days ago Sebashish • 0
3
votes
2
replies
154
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 3 days ago by ★ 3.9k • written 5 days ago by ▴ 10
0
votes
1
reply
80
views
FDR via q-value
qvalue
updated 3 days ago by 65k • written 5 days ago by • 0
0
votes
2
replies
152
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 days ago • updated 3 days ago catv • 0
0
votes
3
replies
102
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 5 days ago by 65k • written 6 days ago by ▴ 30
1
vote
0
replies
199
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
6 days ago • updated 5 days ago BioinfGuru ▴ 30
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
6 days ago prity6459 • 0
2
votes
2
replies
139
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 6 days ago by 65k • written 6 days ago by • 0
0
votes
4
replies
131
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago sropri • 0
1
vote
4
replies
143
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 2 days ago by 65k • written 6 days ago by • 0
0
votes
3
replies
128
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 6 days ago by 50k • written 6 days ago by • 0
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 6 days ago by 3.8k • written 6 days ago by • 0
0
votes
1
reply
83
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by ★ 1.9k • written 7 days ago by • 0
0
votes
1
reply
89
views
rlog transformation
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 7 days ago by • 0
3
votes
1
reply
117
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 days ago by 50k • written 7 days ago by • 0
1
vote
2
replies
180
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
7 days ago • updated 6 days ago Le • 0
1
vote
2
replies
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
7 days ago • updated 6 days ago Sherin • 0
0
votes
1
reply
78
views
Input Question for deseq.r
RSeqAn
updated 7 days ago by ★ 4.0k • written 7 days ago by • 0
4
votes
6
replies
327
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago Jonathan ▴ 10
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 5 days ago lonn • 0
0
votes
1
reply
97
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
114
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by ★ 4.0k • written 8 days ago by • 0
0
votes
7
replies
244
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
8 days ago • updated 2 days ago hortense96 • 0
205 results • Page 1 of 5
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
United States, just now
Germany, 1 minute ago
France, 2 minutes ago
United States, 9 minutes ago
Argentina, 11 minutes ago
Traffic: 1057 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