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Showing :
rlog
•
reset
3
votes
3
replies
976
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 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
dario.beraldi
• 0
1
vote
1
reply
757
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
2.1k
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
41k • 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 2.5 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
835
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
806
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
786
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
Frederik Ziebell
▴ 20
1
vote
2
replies
953
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
6.7 years ago • updated 6.6 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
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
8.2 years ago • updated 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
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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