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rlog
•
reset
3
votes
3
replies
987
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 17 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 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
dario.beraldi
• 0
1
vote
1
reply
771
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
BT
▴ 10
1
vote
2
replies
1.1k
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
42k • written 2.4 years ago by
celiburgos
• 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 5 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 2.5 years ago by
Michael Love
42k • written 2.5 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 2.6 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
42k • written 2.7 years ago by
Diamond
• 0
1
vote
1
reply
855
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
updated 3.2 years ago by
Michael Love
42k • written 3.2 years ago by
Fischer-philipp
▴ 30
8
votes
8
replies
1.3k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2
rlog
4.0 years ago
Zach Roe
▴ 10
1
vote
2
replies
816
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 4.6 years ago by
Michael Love
42k • written 4.6 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
42k • written 4.8 years ago by
mschmidt
▴ 10
0
votes
3
replies
793
views
Normalisation upstream rlog
deseq2
rlog
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
zhang.jianhai
▴ 10
0
votes
15
replies
2.8k
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
Frederik Ziebell
▴ 20
1
vote
2
replies
971
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
6.7 years ago • updated 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
6.7 years ago
pecot
• 0
2
votes
2
replies
2.7k
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
42k • 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 7.8 years ago by
Michael Love
42k • written 7.8 years ago by
longwoodSequencer
• 0
0
votes
3
replies
7.4k
views
What does DESeq2 rlog() return exactly?
deseq2
rlog
rlog transformation
8.2 years ago
lanhuong
▴ 20
3
votes
4
replies
2.1k
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
2.7k
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
42k • 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
42k • written 9.0 years ago by
snsansom
▴ 20
0
votes
1
reply
2.9k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2
rlog
varianceStabilizingTransformation
lfproc
updated 9.1 years ago by
Michael Love
42k • written 9.1 years ago by
katja
• 0
27 results • Page
1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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