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2
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146
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Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
written 4 weeks ago by
kiqbal
• 0
2
votes
1
reply
444
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 8 months ago by
swbarnes2
★ 1.2k • written 8 months ago by
Hicham
• 0
1
vote
5
replies
2.4k
views
is it possible to use TPM in DESeq2 ?
counts
Normalization
DESeq2
updated 8 months ago by
swbarnes2
★ 1.2k • written 8 months ago by
Hicham
• 0
0
votes
3
replies
420
views
dealing with outliers (deseq2)
maxcooks
outliers
zero
counts
DESeq2
updated 10 months ago by
Michael Love
39k • written 10 months ago by
andreia
▴ 10
0
votes
1
reply
459
views
small RNA counts
counts
SmallRNA
Normalization
updated 13 months ago by
hauken_heyken
▴ 80 • written 14 months ago by
k___
▴ 20
4
votes
4
replies
2.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
14 months ago
k___
▴ 20
0
votes
2
replies
1.7k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 2.2 years ago by
Michael Love
39k • written 2.2 years ago by
m93
• 0
1
vote
8
replies
1.0k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq
DESeq2
outlier
counts
DE analysis
updated 2.7 years ago by
Kevin Blighe
3.7k • written 2.7 years ago by
DcL-A
• 0
2
votes
4
replies
2.9k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
3.8 years ago • updated 2.9 years ago
Mozart
▴ 20
0
votes
0
replies
432
views
using gene expression matrix for TCseq package to cluster genes
TCseq
microwarray
cluster
counts
normalization
3.5 years ago
bioyas
▴ 10
5
votes
3
replies
920
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger
normalization
counts
RNA-seq
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Tima Karginov
• 0
2
votes
1
reply
747
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 3.8 years ago by
Rory Stark
★ 4.6k • written 3.9 years ago by
pgontarz
▴ 10
0
votes
4
replies
6.8k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 3.8 years ago by
Ahmed Alhendi
• 0 • written 4.1 years ago by
chiara.facciotto
• 0
0
votes
7
replies
868
views
Results table completely wrong for specified contrast of
DESeq2
logfoldchange
counts
updated 4.0 years ago by
Michael Love
39k • written 4.0 years ago by
A
▴ 40
0
votes
7
replies
1.3k
views
Count filter for differential expression
edger
limma
counts
updated 4.1 years ago by
Gordon Smyth
47k • written 4.1 years ago by
kaur
• 0
2
votes
4
replies
1.0k
views
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
deseq2
edger
fpkm
counts
fc
updated 4.3 years ago by
Gordon Smyth
47k • written 4.3 years ago by
ZihaoXing
• 0
1
vote
2
replies
722
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2
edger
fpkm
counts
TCGA
updated 4.3 years ago by
Gordon Smyth
47k • written 4.3 years ago by
ZihaoXing
• 0
0
votes
3
replies
2.1k
views
Handling pseudogenes in RNA-seq
rna-seq
pseudogenes
STAR
counts
updated 4.6 years ago by
Levi Waldron
1.1k • written 4.6 years ago by
supremerulersuraj
• 0
2
votes
3
replies
1.4k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind
chipseq
counts
peaks
bedtools
updated 20 months ago by
Rory Stark
★ 4.6k • written 4.8 years ago by
Ni-Ar
▴ 10
1
vote
1
reply
664
views
How to compare RNA-seq counts matrices from different aligners ?
rnaseq
counts
alignement
4.8 years ago
Aurora
▴ 20
2
votes
3
replies
2.2k
views
Deseq2: padj value changes with varying alpha
deseq2
counts
rnaseq
updated 5.3 years ago by
Michael Love
39k • written 5.3 years ago by
yoursbassanio
▴ 10
0
votes
5
replies
4.2k
views
unable to find an inherited method for function counts for signature DESeqTransform
deseq2
counts
DESeqtransform
variance
deviation
updated 5.3 years ago by
Michael Love
39k • written 5.3 years ago by
Casper Peters
• 0
0
votes
3
replies
1.0k
views
DESeq2 ComputeSumFactors extract normalized counts
deseq2
normalization
counts
updated 5.4 years ago by
Michael Love
39k • written 5.4 years ago by
herrmannmaria94
• 0
0
votes
0
replies
638
views
Combined strand specific and unstranded samples
strand
rnaseq
differential gene expression
batch effect
counts
5.4 years ago
lirongrossmann
▴ 70
4
votes
2
replies
1.4k
views
Help: extract counts from RNA-seq .bam/.bai files
counts
edger
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
mat149
▴ 70
6
votes
4
replies
2.8k
views
Can edgeR TMM normalization be used for other count data?
edgeR
tmm
normalization
counts
updated 5.8 years ago by
James W. MacDonald
62k • written 5.8 years ago by
jol.espinoz
▴ 40
0
votes
1
reply
1.2k
views
IRanges object from count matrix
genomicranges
iranges
featurecounts
counts
rnaseq
updated 5.9 years ago by
Hervé Pagès
16k • written 6.0 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
819
views
small RNAs quantification
smallrna
counts
6.3 years ago
ribioinfo
▴ 100
2
votes
1
reply
3.0k
views
DESeq2 Input format
deseq2
counts
updated 6.4 years ago by
Michael Love
39k • written 6.4 years ago by
uzer
• 0
1
vote
3
replies
1.0k
views
DESeq2: Do basemean values take into account interaction effects?
deseq2
counts
normalized counts
updated 6.5 years ago by
Steve Lianoglou
13k • written 6.5 years ago by
snamjoshi87
▴ 40
1
vote
4
replies
946
views
comparing transcripts expression between conditions
salmon
transcripts
significance
counts
6.5 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
1.4k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2
chipseq
counts
log2fc
error
updated 6.6 years ago by
Michael Love
39k • written 6.6 years ago by
robin.uchiyama
• 0
3
votes
1
reply
1.0k
views
window counts in csaw
csaw
counts
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
nobishvarghese
• 0
6
votes
12
replies
12k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 6.7 years ago by
Michael Love
39k • written 6.7 years ago by
wannes.nauwynck
▴ 10
4
votes
3
replies
7.1k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 6.9 years ago by
Michael Love
39k • written 6.9 years ago by
hechtp
▴ 10
1
vote
3
replies
2.5k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
7.0 years ago
Jon Bråte
▴ 240
2
votes
4
replies
2.0k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps
RNAseq
annotation
counts
7.0 years ago
bioprog
• 0
2
votes
5
replies
2.7k
views
Limma/DESeq2: Statistic and readcount of biological replicates
normalization
limma
deseq2
counts
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Radek
▴ 90
1
vote
5
replies
1.4k
views
deseq2 normalized data
regression
deseq2
counts
updated 7.4 years ago by
Michael Love
39k • written 7.4 years ago by
akp
• 0
1
vote
1
reply
5.2k
views
Not full rank design using Deseq2
deseq2
design
counts
updated 8.0 years ago by
Michael Love
39k • written 8.0 years ago by
Rainy Gorilla
▴ 30
0
votes
1
reply
1.1k
views
DEXSeq error: Count files do not correspond to the flattened annotation file
DEXSeq
counts
gff
8.2 years ago
Assa Yeroslaviz
★ 1.5k
3
votes
5
replies
6.8k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 8.2 years ago by
Steve Lianoglou
13k • written 8.2 years ago by
Peter Crisp
▴ 10
42 results • Page
1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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