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rlog
•
reset
3
votes
3
replies
968
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 16 months ago by
Bioinformatics-414
• 0
3
votes
4
replies
1.5k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2
Normalization
rlog
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
dario.beraldi
• 0
1
vote
1
reply
750
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
BT
▴ 10
1
vote
2
replies
1.0k
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.3 years ago
Bex
• 0
1
vote
3
replies
1.5k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
celiburgos
• 0
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 4 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
6
votes
4
replies
1.5k
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
2
votes
4
replies
2.5k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 2.3 years ago by
Sam
• 0 • written 2.5 years ago by
JB
▴ 10
0
votes
3
replies
2.3k
views
Different PCA results when using rlog and vst transformations
vsn
DESeq2
rlog
BatchEffect
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
Diamond
• 0
1
vote
1
reply
829
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
Fischer-philipp
▴ 30
8
votes
8
replies
1.2k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2
rlog
4.0 years ago
Zach Roe
▴ 10
1
vote
2
replies
802
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 4.4 years ago by
Steve Lianoglou
★ 13k • written 4.4 years ago by
zhang.jianhai
▴ 10
0
votes
1
reply
2.7k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
juheon.maeng
• 0
1
vote
7
replies
1.2k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2
rlog
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
mschmidt
▴ 10
0
votes
3
replies
783
views
Normalisation upstream rlog
deseq2
rlog
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
zhang.jianhai
▴ 10
0
votes
15
replies
2.7k
views
rlog not found
rlog
rlog transformation
6.0 years ago
crowsreign42
• 0
0
votes
4
replies
2.0k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2
rlog
6.3 years ago • updated 6.2 years ago
Frederik Ziebell
▴ 20
1
vote
2
replies
945
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2
rlog
deseq
6.4 years ago
sreibe
• 0
0
votes
6
replies
3.2k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
6.6 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
pecot
• 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 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
Zach Roe
▴ 10
6
votes
4
replies
3.7k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
longwoodSequencer
• 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
4
replies
2.0k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2
cummerbund
rlog
fpkm
clustering
8.3 years ago
Jon Bråte
▴ 250
2
votes
5
replies
2.6k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2
rlog
updated 8.6 years ago by
Michael Love
41k • written 8.6 years ago by
sjmonkley
▴ 40
4
votes
4
replies
2.2k
views
Dependence of rlog transformed value range on number of samples
deseq2
rlog
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
snsansom
▴ 20
0
votes
1
reply
2.8k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2
rlog
varianceStabilizingTransformation
lfproc
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
katja
• 0
27 results • Page
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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