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Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
just now
james.zhang20
• 0
0
votes
1
reply
31
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
10
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
2 hours ago
shepherl
3.8k
0
votes
0
replies
24
views
Empty table plot using plotGseaTable()
fgsea
4 hours ago • updated 1 hour ago
Chris
• 0
0
votes
3
replies
77
views
Store output of matchPWM()
biostrings
Biostrings
updated 3 hours ago by
James W. MacDonald
65k • written 7 hours ago by
mat149
▴ 70
0
votes
3
replies
132
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 hour 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 21 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 19 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
147
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 4 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
177
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
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
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
1
vote
4
replies
286
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago
winwater0928
• 0
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
2
replies
225
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
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
11 days ago • updated 3 hours ago
Chris
• 0
0
votes
3
replies
148
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 13 days ago by
Alessia
• 0
1
vote
2
replies
687
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 1 day ago
Chris
• 0
0
votes
4
replies
231
views
Minfi - estimatecellscount
min
minfi
updated 2 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
1
vote
4
replies
419
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 3 hours ago
JKim
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 1 day ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 1 day ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
44 results • Page
1 of 1
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Replies
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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