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Votes
0
votes
4
replies
306
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
11 days ago • updated 3 days ago
Efra
• 0
0
votes
1
reply
122
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
Yuqin
• 0
1
vote
1
reply
123
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 11 days ago by
Michael Love
41k • written 11 days ago by
Emma
• 0
4
votes
7
replies
331
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
1
vote
1
reply
139
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
zoheir.alayash
▴ 10
0
votes
1
reply
129
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 12 days ago by
Gordon Smyth
50k • written 14 days ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
164
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
14 days ago • updated 12 days ago
feather-W
• 0
0
votes
2
replies
214
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
2
votes
2
replies
200
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 11 days ago
elesofi
• 0
0
votes
1
reply
131
views
problem with ClusterRepro function
WGCNA
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Antonio.Aubry
• 0
0
votes
4
replies
356
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 14 days ago by
Michael Love
41k • written 15 days ago by
Jad
• 0
2
votes
2
replies
192
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
15 days ago
Sabiha
▴ 20
0
votes
2
replies
167
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
15 days ago • updated 14 days ago
kcarey
• 0
0
votes
7
replies
343
views
DESeq2 filtering vs edgeR filtering
DESeq2
16 days ago • updated 2 days ago
fr8712ca-s
• 0
0
votes
2
replies
249
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 16 days ago by
gglatzer
• 0
0
votes
2
replies
176
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
16 days ago • updated 15 days ago
Sam
▴ 10
2
votes
1
reply
193
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
hemantcnaik
• 0
1
vote
1
reply
168
views
i'm not getting any differentially expressed genes.
DESeq2
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Marilyn
• 0
0
votes
1
reply
166
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 17 days ago by
BioinfoMug
• 0
0
votes
1
reply
145
views
Exact same results in Diffbind with different normalization methods
DiffBind
17 days ago • updated 12 days ago
red_bricks
▴ 50
0
votes
0
replies
102
views
FELLA plotGraph function won't change the legend
FELLA
17 days ago
yuhang
• 0
0
votes
0
replies
101
views
medips-output
ngsReports
MEDIPS
17 days ago
subhiksha
• 0
0
votes
0
replies
98
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
17 days ago
bocsci11
• 0
0
votes
0
replies
87
views
The graphical interface of FELLA doesn't work
FELLA
18 days ago
yuhang
• 0
0
votes
0
replies
95
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
18 days ago
jean-christophe.helbling
• 0
0
votes
1
reply
109
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
maltethodberg
▴ 170
0
votes
4
replies
217
views
Error in classify_gene_pairs
syntenet
doubletrouble
18 days ago • updated 17 days ago
hfyuan2016
• 0
1
vote
1
reply
162
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.0k • written 18 days ago by
synat.keam
• 0
0
votes
0
replies
111
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
21 days ago
Henry
• 0
1
vote
5
replies
333
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
21 days ago • updated 11 days ago
Gerhard Thallinger
▴ 180
0
votes
1
reply
153
views
Rcpp compilation error
Release
Rcpp
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
113
views
Rain error: invalid annotation of time points
rain
21 days ago
mpuli011
• 0
0
votes
2
replies
274
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 days ago • updated 20 days ago
Viktor Thiel
• 0
0
votes
0
replies
105
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
21 days ago
Felix
• 0
0
votes
1
reply
138
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
187
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
21 days ago
thomas
• 0
1
vote
1
reply
144
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
ronin
• 0
0
votes
8
replies
296
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
22 days ago • updated 21 days ago
michelafrancesconi8
• 0
0
votes
0
replies
111
views
News:
Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
22 days ago
cv.jam.zhxf17875
• 0
0
votes
1
reply
152
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 22 days ago by
ATpoint
★ 4.0k • written 22 days ago by
Sneha
• 0
0
votes
6
replies
326
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
22 days ago • updated 3 days ago
Lily Cheang
• 0
1
vote
4
replies
235
views
DESeq2 Replicates
DESeq2
RNASeq
22 days ago
kcarey
• 0
2
votes
6
replies
267
views
Factor vs Character in design
DESeq2
22 days ago
James Aiden
• 0
3
votes
8
replies
425
views
Constrast for Time Course Experiments using Limma
limma
23 days ago • updated 21 days ago
dl17032000
• 0
0
votes
1
reply
147
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
23 days ago • updated 2 days ago
shepherl
3.8k
0
votes
0
replies
111
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
23 days ago • updated 10 days ago
Giovanni Calice
▴ 160
0
votes
0
replies
146
views
Job:
Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics
JobPosting
SingleCell
Spatial
SpatialExperiment
24 days ago
Peter Hickey
▴ 670
3
votes
4
replies
290
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 23 days ago by
Gordon Smyth
50k • written 24 days ago by
Jack S.
▴ 50
0
votes
0
replies
121
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
Andrew
• 0
0
votes
1
reply
179
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 24 days ago by
belinda.phipson
▴ 40 • written 24 days ago by
saad.malik
• 0
194 results • Page
2 of 4
Recent ...
Replies
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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