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9
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12
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7.7k
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Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 47 minutes ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 14 hours ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
5
votes
9
replies
770
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
7 days ago • updated 1 hour ago
Chris
• 0
4
votes
8
replies
280
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 15 hours ago by
Peter Hickey
▴ 740 • written 7 days ago by
Juan Higareda
• 0
3
votes
3
replies
122
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
6 days ago • updated 5 hours ago
jacques.imbert
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 21 hours ago
shepherl
3.8k
2
votes
3
replies
618
views
DESeq2 setting significant p-value
DESeq2
updated 2 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
2
replies
50
views
Error in champ.load(): The following specified files do not exist
ChAMP
19 hours ago • updated 29 minutes ago
Sherin
• 0
0
votes
0
replies
12
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
4 hours ago
Alessia
• 0
0
votes
3
replies
153
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 3 hours ago by
ATpoint
★ 4.0k • written 6 days ago by
schlumbohm
• 0
0
votes
1
reply
55
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 3 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
1
reply
34
views
Input Question for deseq.r
RSeqAn
updated 3 hours ago by
ATpoint
★ 4.0k • written 20 hours ago by
Nina
• 0
0
votes
0
replies
29
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
1 day ago • updated 23 hours ago
ussarizona
• 0
0
votes
2
replies
82
views
FilterByExpr low counts with small sample size
edgeR
22 hours ago • updated 10 minutes ago
Jonathan
▴ 10
0
votes
2
replies
865
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 21 hours ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
6
replies
138
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 16 hours ago by
Gordon Smyth
50k • written 1 day ago by
hortense96
• 0
0
votes
0
replies
17
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
7 hours ago
Le
• 0
0
votes
0
replies
28
views
Log-cpm values from limma
limma
edgeR
RNASeq
7 hours ago
Shaimaa Gamal
• 0
0
votes
0
replies
15
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
5 hours ago
09191919
• 0
0
votes
2
replies
269
views
DESeq filtering specific to contrasts
DESeq2
updated 5 hours ago by
Carlin95
• 0 • written 8 weeks ago by
Emma
• 0
0
votes
0
replies
17
views
rlog transformation
DESeq2
5 hours ago
ishij9717
• 0
21 results • Page
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Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist
by
Sherin
• 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2
by
Elizabeth
• 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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