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1
vote
6
replies
946
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by
Erin Yu
• 0
4
votes
4
replies
440
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
1
vote
4
replies
681
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
7 months ago
andrew.b.kleist
▴ 10
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.2 years ago by
tleona3
• 0
5
votes
6
replies
857
views
ASpli checks fail on Linux due to missing dependency to statmod
ASpli
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
martin.grigorov
▴ 10
1
vote
2
replies
357
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
Kim
• 0
3
votes
2
replies
570
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
mckinlee.salazar
• 0
1
vote
2
replies
469
views
Assess fit of variance prior
limma
updated 4 months ago by
Gordon Smyth
50k • written 5 months ago by
Frederik Ziebell
▴ 20
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago
Luis
• 0
0
votes
6
replies
363
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Faisal
• 0
0
votes
3
replies
512
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
jovel_juan
▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 5 months ago by
Gordon Smyth
50k • written 8.2 years ago by
Radek
▴ 90
5
votes
5
replies
449
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago
baptiste
▴ 20
0
votes
9
replies
855
views
estimateDisp() error
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
ASNbioinf
• 0
5
votes
2
replies
574
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
1
vote
2
replies
313
views
Impute does not work
impute
10 weeks ago
Laura
• 0
2
votes
6
replies
365
views
Factor vs Character in design
DESeq2
9 weeks ago
James Aiden
• 0
0
votes
2
replies
369
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 9 weeks ago by
ATpoint
★ 4.1k • written 10 weeks ago by
Suvi
• 0
1
vote
2
replies
435
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Jurgen
• 0
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by
Mingkee
• 0 • written 6.8 years ago by
yura.grabovska
▴ 30
8
votes
6
replies
480
views
DGE analysis with LIMMA
limma
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Amit
• 0
1
vote
3
replies
419
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
0
votes
4
replies
277
views
DEG with low counts
DESeq2
updated 21 days ago by
Michael Love
42k • written 25 days ago by
Rajat
• 0
6
votes
9
replies
797
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 3 months ago by
alexander3
• 0 • written 3 months ago by
Amparo
• 0
1
vote
3
replies
343
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
10 weeks ago • updated 9 weeks ago
I-Hsuan Lin
▴ 10
1
vote
4
replies
749
views
MDS plot edgeR
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
jbono
▴ 10
2
votes
3
replies
1.2k
views
Problem with function combine regarding merging two data frames based on their common rows
bioconductor
merge data frames
combine
biocgenerics
8.5 years ago • updated 6 months ago
Konstantinos Yeles
▴ 80
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
65k • written 11 months ago by
kyliecode
• 0
0
votes
2
replies
423
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 5 months ago by
Stephanie M. Gogarten
▴ 870 • written 5 months ago by
Mindy wang
• 0
0
votes
2
replies
888
views
News:
List of Deprecated Packages for Bioc3.17
Bioconductor
Deprecation
Devel
devel
13 months ago • updated 11 months ago
shepherl
3.9k
1
vote
2
replies
669
views
unable to retrieve certain packages from bioconductor 3.15
Bioconductor
biocondu
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Ashton
▴ 10
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 4 months ago by
picasa1983
• 0 • written 2.3 years ago by
Victor
• 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
2
votes
1
reply
271
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
3 months ago
mat149
▴ 70
0
votes
2
replies
853
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
0
votes
2
replies
489
views
EdgeR FTest
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
nawaz.u.toyama
• 0
1
vote
10
replies
468
views
Obtaining pheno data from CEL files
GEO
affy
5 weeks ago • updated 4 weeks ago
Kurtis
• 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
3
votes
2
replies
452
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
S
• 0
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges
genomicfeatures
translation
updated 3 months ago by
russ.bainer
▴ 10 • written 8.4 years ago by
madsheilskov
▴ 10
4
votes
6
replies
760
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago
isaac.vock
• 0
1
vote
3
replies
602
views
Read Count Normalisation and validation of analysis
DifferentialExpression
DESeq2
written 4 months ago by
Dinesh
• 0
0
votes
4
replies
3.6k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 10 months ago by
Marco
• 0 • written 4.5 years ago by
mathai.c
• 0
2
votes
2
replies
438
views
Remove duplicates of colData in TreeSummarizedExperiment
dplyr
TreeSummarizedExperiment
updated 7 months ago by
Michael Love
42k • written 7 months ago by
question_guy
• 0
1
vote
6
replies
502
views
GSVA on separate healthy and disease datasets
GSVA
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Lucy
▴ 60
2
votes
3
replies
3.1k
views
Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by
pbachali
▴ 50
0
votes
4
replies
200
views
flowStats Search Error
flowStats
updated 23 days ago by
shepherl
3.9k • written 24 days ago by
tholmes
• 0
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
0
votes
3
replies
465
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
1,744 results • Page
3 of 35
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Replies
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
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