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0
votes
0
replies
10
views
unable to install RBGL
#RBGL
2 hours ago
baldwinh555
• 0
0
votes
0
replies
30
views
DEXSeq python scripts count too few reads
splicing
reads
DEXSeq
6 hours ago • updated 2 hours ago
NIK
• 0
0
votes
2
replies
65
views
RPX PXDataset error
PRIDE
rpx
PXDataset
updated 6 hours ago by
Laurent Gatto
1.5k • written 7 days ago by
gianluigi.caltabiano
• 0
0
votes
0
replies
24
views
Not obtaining significant Gene Ontology Biological Process hits
clusterProfiler
7 hours ago
Jordan
• 0
0
votes
2
replies
57
views
Package name already exists due to previous issue
Bioconductor
updated 7 hours ago by
shepherl
3.1k • written 1 day ago by
Daan
• 0
0
votes
1
reply
41
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 8 hours ago by
James W. MacDonald
59k • written 2 days ago by
rsnorman
• 0
1
vote
4
replies
84
views
CPM after RUVseq
RUVSeq
CPM
Normalization
updated 3 hours ago by
James W. MacDonald
59k • written 3 days ago by
Jess
• 0
0
votes
0
replies
23
views
Job:
Bioconductor Community Manager
Community
Teaching
Bioconductor
23 hours ago • updated 9 hours ago
Matthew Ritchie
▴ 1000
3
votes
3
replies
41
views
Merging two plated in R
dese
DESeq2
updated 9 hours ago by
James W. MacDonald
59k • written 9 hours ago by
lmrogers34
• 0
0
votes
2
replies
250
views
layout has more positions than samples but omixerRand doesn't randomize the samples
Omixer
13 months ago • updated 10 hours ago
Lluís Revilla Sancho
▴ 660
1
vote
4
replies
91
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 13 hours ago by
Kevin Blighe
3.5k • written 1 day ago by
beslinail
• 0
1
vote
1
reply
45
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 16 hours ago by
ATpoint
★ 1.2k • written 17 hours ago by
Dimitris
• 0
0
votes
1
reply
180
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
updated 18 hours ago by
Robert Castelo
★ 2.9k • written 8 months ago by
Guandong Shang
▴ 20
3
votes
3
replies
100
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 18 hours ago by
Gordon Smyth
45k • written 1 day ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
40
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression
DiffBind
1 day ago • updated 10 hours ago
Luca
• 0
0
votes
6
replies
115
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
1 day ago • updated 14 hours ago
nabiyogesh
▴ 10
2
votes
6
replies
150
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq
DESeq2
3 days ago • updated 1 day ago
andrebolerbarros
▴ 10
0
votes
1
reply
48
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 1 day ago by
Basti
▴ 280 • written 1 day ago by
marc.tormo
• 0
2
votes
2
replies
50
views
How to run GSVA with partially NA genes
GSVA
1 day ago • updated 22 hours ago
blakebowen
• 0
0
votes
2
replies
183
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 20 days ago by
curiousmind007
• 0
0
votes
2
replies
84
views
Using limma to read Illumina HT-12 v4 data
limma
updated 2 days ago by
Gordon Smyth
45k • written 3 days ago by
orbitofrontal
• 0
0
votes
4
replies
127
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 2 days ago by
ATpoint
★ 1.2k • written 5 days ago by
Bogdan
▴ 640
0
votes
2
replies
65
views
R: problem with running time-series analysis software: Mfuzz
time-series
mfuzz
replace=FALSE
3 days ago
soda
▴ 80
1
vote
4
replies
117
views
ashr vs apeglm for interaction data
lfcShrink
DESeq2
6 days ago • updated 1 day ago
Ali Barry
▴ 30
2
votes
4
replies
100
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219
oligo
AffymetrixChip
4 days ago
Yang Shi
• 0
1
vote
5
replies
134
views
UniprotKB AC/ID to Entrez ID Conversion
ID
Uniprot
EntrezID
4 days ago • updated 1 day ago
tom.kloter
• 0
2
votes
2
replies
77
views
how to make a group to apply the data to CAMERA
CAMERA
4 days ago • updated 2 days ago
Akira
• 0
4
votes
10
replies
221
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
5 days ago • updated 4 days ago
Yang Shi
• 0
4
votes
6
replies
181
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
6 days ago • updated 1 day ago
mohammedtoufiq91
▴ 10
1
vote
4
replies
208
views
different results in DESeq2 when comparing groups in two ways
DESeq2
6 days ago • updated 5 days ago
zohreh.fazelan
• 0
0
votes
1
reply
94
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 4 days ago by
ATpoint
★ 1.2k • written 5 days ago by
johnmcma
▴ 10
1
vote
1
reply
70
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
5 days ago • updated 4 days ago
takemoto
• 0
3
votes
5
replies
130
views
Print EnhancedVolcano Plot as jpeg or similar in R Notebook
EnhancedVolcano
updated 5 days ago by
Kevin Blighe
3.5k • written 5 days ago by
Bine
▴ 20
0
votes
0
replies
35
views
Regarding installing RAMA, BRIDGE, and iterative BMA packages in MultiExperiment Viewer (MeV).
MeV+R
MeV
5 days ago
Souvik
• 0
5
votes
5
replies
2.3k
views
how to understand cpm=1 and how filterByExpr works?
edger
updated 6 days ago by
gowthamee
• 0 • written 20 months ago by
linouhao
▴ 20
0
votes
1
reply
57
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization
edgeR
updated 5 days ago by
Gordon Smyth
45k • written 6 days ago by
kevin
• 0
3
votes
4
replies
126
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
6 days ago • updated 5 days ago
Yang Shi
• 0
1
vote
1
reply
68
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 4 days ago by
Gordon Smyth
45k • written 6 days ago by
margo
• 0
2
votes
1
reply
64
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 6 days ago by
James W. MacDonald
59k • written 6 days ago by
nhaus
• 0
0
votes
3
replies
164
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
7 weeks ago • updated 6 days ago
ramonfallon
• 0
0
votes
1
reply
88
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
6 days ago • updated 3 days ago
Gyan Prakash Mishra
• 0
0
votes
1
reply
55
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 6 days ago by
Basti
▴ 280 • written 6 days ago by
ramonfallon
• 0
3
votes
3
replies
115
views
edgeR: the F-statistics changed after removing lowly expressed gene
glmQLFTest
edgeR
updated 6 days ago by
Gordon Smyth
45k • written 6 days ago by
Pei
• 0
0
votes
13
replies
305
views
EnrichGO not working with db created from annotationhub
clusterProfiler
AnnotationHubData
GO
updated 6 days ago by
Guido Hooiveld
★ 3.2k • written 10 days ago by
Lucía
• 0
2
votes
1
reply
67
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 7 days ago by
swbarnes2
★ 1.0k • written 7 days ago by
Hicham
• 0
0
votes
0
replies
30
views
Rcpp std::chdir
Rcpp
7 days ago
ullrich
▴ 10
0
votes
1
reply
62
views
DESeq2 paired design: Differential list comparing fold changes
DESeq2
updated 7 days ago by
swbarnes2
★ 1.0k • written 7 days ago by
athira
• 0
0
votes
3
replies
105
views
DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change introduced between version 2.14 and 3.4.11
DiffBind
updated 7 days ago by
Rory Stark
★ 4.4k • written 7 days ago by
chrarnold
• 0
3
votes
4
replies
154
views
DESeq2: Extracting Averaged Counts Information from dds and rld
DESeq2
13 days ago • updated 7 days ago
vanbelj
▴ 10
0
votes
6
replies
200
views
DESeq2, Calculate the size factor by using median-of-ratio
median
DESeq2
12 days ago • updated 7 days ago
KEREN
• 0
262 results • Page
1 of 6
Recent ...
Replies
Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue
by
shepherl
3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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