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Showing :
rlog
•
reset
3
votes
3
replies
385
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 5 months ago by
Bioinformatics-414
• 0
3
votes
4
replies
866
views
Large difference between naive log2 and rlog transformation of count data
DESeq2
Normalization
rlog
updated 14 months ago by
Michael Love
40k • written 14 months ago by
dario.beraldi
• 0
1
vote
1
reply
441
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 16 months ago by
Michael Love
40k • written 16 months ago by
BT
▴ 10
1
vote
2
replies
572
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
16 months ago
Bex
• 0
1
vote
3
replies
856
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 16 months ago by
Michael Love
40k • written 16 months ago by
celiburgos
• 0
3
votes
3
replies
910
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
written 17 months ago by
mohammedtoufiq91
▴ 10
6
votes
4
replies
1.0k
views
Which rlog should I use for DESeq2 analysis
samples
rlog
DESeq2
updated 18 months ago by
Michael Love
40k • written 18 months ago by
rafaelsolersanblas
▴ 50
2
votes
4
replies
1.3k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 16 months ago by
Sam
• 0 • written 19 months ago by
JB
▴ 10
0
votes
3
replies
1.3k
views
Different PCA results when using rlog and vst transformations
vsn
DESeq2
rlog
BatchEffect
updated 21 months ago by
Michael Love
40k • written 21 months ago by
Diamond
• 0
1
vote
1
reply
517
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
updated 2.3 years ago by
Michael Love
40k • written 2.3 years ago by
Fischer-philipp
▴ 30
8
votes
8
replies
788
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2
rlog
3.1 years ago
Zach Roe
▴ 10
1
vote
2
replies
515
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 3.5 years ago by
Steve Lianoglou
13k • written 3.5 years ago by
zhang.jianhai
▴ 10
0
votes
1
reply
1.9k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 3.6 years ago by
Michael Love
40k • written 3.6 years ago by
juheon.maeng
• 0
1
vote
7
replies
871
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2
rlog
updated 3.9 years ago by
Michael Love
40k • written 3.9 years ago by
mschmidt
▴ 10
0
votes
3
replies
548
views
Normalisation upstream rlog
deseq2
rlog
updated 4.2 years ago by
Michael Love
40k • written 4.2 years ago by
zhang.jianhai
▴ 10
0
votes
15
replies
2.0k
views
rlog not found
rlog
rlog transformation
5.1 years ago
crowsreign42
• 0
0
votes
4
replies
1.4k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2
rlog
5.4 years ago • updated 5.3 years ago
Frederik Ziebell
▴ 10
1
vote
2
replies
685
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2
rlog
deseq
5.5 years ago
sreibe
• 0
0
votes
6
replies
2.3k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
5.7 years ago
lirongrossmann
▴ 80
0
votes
9
replies
1.3k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2
lfcshrink
rlog
5.7 years ago
pecot
• 0
2
votes
2
replies
2.3k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2
rlog
variancestabilizingtransformation
DESeq
updated 6.3 years ago by
Michael Love
40k • written 6.3 years ago by
Zach Roe
▴ 10
6
votes
4
replies
3.1k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 6.8 years ago by
Michael Love
40k • written 6.8 years ago by
longwoodSequencer
• 0
0
votes
3
replies
6.7k
views
What does DESeq2 rlog() return exactly?
deseq2
rlog
rlog transformation
7.2 years ago
lanhuong
▴ 20
3
votes
4
replies
1.6k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2
cummerbund
rlog
fpkm
clustering
7.4 years ago
Jon Bråte
▴ 250
2
votes
5
replies
2.3k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2
rlog
updated 7.7 years ago by
Michael Love
40k • written 7.7 years ago by
sjmonkley
▴ 40
4
votes
4
replies
1.8k
views
Dependence of rlog transformed value range on number of samples
deseq2
rlog
updated 8.1 years ago by
Michael Love
40k • written 8.1 years ago by
snsansom
▴ 20
0
votes
1
reply
2.2k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2
rlog
varianceStabilizingTransformation
lfproc
updated 8.1 years ago by
Michael Love
40k • written 8.1 years ago by
katja
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Gordon Smyth
47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind
by
Chris
• 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind
by
Chris
• 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting
by
phelankj
• 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting
by
James W. MacDonald
63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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