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5
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Deseq2 and Normalization of RNA sequencing data
DESeq2
22 minutes ago • updated 21 minutes ago
kcarey
• 0
0
votes
0
replies
7
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
33 minutes ago • updated 10 minutes ago
james.zhang20
• 0
0
votes
1
reply
35
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 hours ago by
ATpoint
★ 4.1k • written 2 hours ago by
angelathuynh5
• 0
0
votes
0
replies
11
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
3 hours ago
shepherl
3.8k
0
votes
0
replies
25
views
Empty table plot using plotGseaTable()
fgsea
4 hours ago • updated 2 hours ago
Chris
• 0
0
votes
3
replies
81
views
Store output of matchPWM()
biostrings
Biostrings
updated 4 hours ago by
James W. MacDonald
65k • written 7 hours ago by
mat149
▴ 70
0
votes
3
replies
146
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
2
replies
55
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
written 22 hours ago by
Yveto
• 0
0
votes
0
replies
20
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
13 hours ago
Ian D.
▴ 70
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 20 hours ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
194
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
3
votes
4
replies
149
views
Help with error using camera() in limma
CAMERA
limma
1 day ago
Chris
• 0
1
vote
1
reply
69
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
62
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Aurora
• 0
0
votes
1
reply
71
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
0
replies
38
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
1
reply
49
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
bounlu
• 0
0
votes
1
reply
68
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
Dev
• 0
2
votes
2
replies
146
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
2 days ago
Chris
• 0
0
votes
3
replies
188
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
0
replies
45
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
2 days ago
Chris
• 0
3
votes
3
replies
180
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
bioinf
▴ 10
1
vote
1
reply
102
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by
Leo Lahti
▴ 40 • written 5 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
173
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Aaliya
• 0
1
vote
3
replies
178
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
107
views
ATACseq merge peaks
DiffBind
updated 5 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 0
1
vote
1
reply
143
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 5 days ago by
Gordon Smyth
50k • written 9 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
275
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
6 days ago • updated 5 days ago
pl23
• 0
2
votes
9
replies
333
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
0
votes
0
replies
72
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
6 days ago
glaciya2018
• 0
1
vote
2
replies
134
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
7 days ago • updated 6 days ago
ATpoint
★ 4.1k
0
votes
1
reply
122
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
0
votes
0
replies
64
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
7 days ago • updated 2 days ago
Sara
• 0
2
votes
5
replies
231
views
get BM error
ensembldb
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
Fara
• 0
2
votes
5
replies
210
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 days ago by
James W. MacDonald
65k • written 8 days ago by
bandconductor
• 0
0
votes
0
replies
67
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
7 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
196
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
287
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago
winwater0928
• 0
3
votes
1
reply
286
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
1
vote
1
reply
156
views
Citation for edgeR user guide
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
k___
▴ 30
0
votes
7
replies
678
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 8 days ago
shepherl
3.8k
1
vote
1
reply
100
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
316
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
0
votes
0
replies
58
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
8 days ago
info
▴ 10
1
vote
4
replies
188
views
minfi::read.metharray.exp
minfiData
minfi
updated 7 days ago by
Basti
▴ 780 • written 9 days ago by
clacarion
• 0
0
votes
2
replies
226
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
8 days ago • updated 6 days ago
shuwangxinze1996
• 0
1
vote
2
replies
970
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 8 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
129
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 8 days ago by
Gordon Smyth
50k • written 9 days ago by
taur.vil
• 0
3
votes
3
replies
207
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
WardDeb
• 0
1
vote
4
replies
207
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 9 days ago by
James W. MacDonald
65k • written 13 days ago by
Mirella Aurora
• 0
45,602 results • Page
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Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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