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rlog
•
reset
3
votes
4
replies
2.0k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2
cummerbund
rlog
fpkm
clustering
8.2 years ago
Jon Bråte
▴ 250
1
vote
2
replies
916
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2
rlog
deseq
6.3 years ago
sreibe
• 0
0
votes
3
replies
7.3k
views
What does DESeq2 rlog() return exactly?
deseq2
rlog
rlog transformation
8.1 years ago
lanhuong
▴ 20
3
votes
3
replies
936
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 15 months ago by
Bioinformatics-414
• 0
6
votes
4
replies
1.4k
views
Which rlog should I use for DESeq2 analysis
samples
rlog
DESeq2
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
rafaelsolersanblas
▴ 50
0
votes
6
replies
3.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
6.5 years ago
lirongrossmann
▴ 80
0
votes
9
replies
1.8k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2
lfcshrink
rlog
6.6 years ago • updated 6.5 years ago
pecot
• 0
0
votes
4
replies
1.9k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2
rlog
6.2 years ago
Frederik Ziebell
▴ 20
1
vote
7
replies
1.2k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2
rlog
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
mschmidt
▴ 10
0
votes
1
reply
2.6k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
juheon.maeng
• 0
1
vote
2
replies
781
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 4.3 years ago by
Steve Lianoglou
★ 13k • written 4.3 years ago by
zhang.jianhai
▴ 10
8
votes
8
replies
1.2k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2
rlog
3.9 years ago
Zach Roe
▴ 10
1
vote
1
reply
803
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
Fischer-philipp
▴ 30
2
votes
4
replies
2.4k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 2.2 years ago by
Sam
• 0 • written 2.5 years ago by
JB
▴ 10
3
votes
4
replies
1.4k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2
Normalization
rlog
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
dario.beraldi
• 0
1
vote
2
replies
991
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.2 years ago
Bex
• 0
1
vote
1
reply
714
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
BT
▴ 10
4
votes
4
replies
1.9k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 3 months ago by
Gordon Smyth
50k • written 2.3 years ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
2.2k
views
Different PCA results when using rlog and vst transformations
vsn
DESeq2
rlog
BatchEffect
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
Diamond
• 0
1
vote
3
replies
1.4k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
celiburgos
• 0
0
votes
3
replies
769
views
Normalisation upstream rlog
deseq2
rlog
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
zhang.jianhai
▴ 10
0
votes
1
reply
2.8k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2
rlog
varianceStabilizingTransformation
lfproc
updated 8.9 years ago by
Michael Love
41k • written 8.9 years ago by
katja
• 0
4
votes
4
replies
2.1k
views
Dependence of rlog transformed value range on number of samples
deseq2
rlog
updated 8.9 years ago by
Michael Love
41k • written 8.9 years ago by
snsansom
▴ 20
2
votes
5
replies
2.6k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2
rlog
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
sjmonkley
▴ 40
6
votes
4
replies
3.6k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
longwoodSequencer
• 0
2
votes
2
replies
2.6k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2
rlog
variancestabilizingtransformation
DESeq
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
Zach Roe
▴ 10
0
votes
15
replies
2.6k
views
rlog not found
rlog
rlog transformation
5.9 years ago
crowsreign42
• 0
27 results • Page
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Answer: Minfi - estimatecellscount
by
James W. MacDonald
65k
Don't filter first. You are likely removing the CpGs that are used to estimate the cell counts.
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
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
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