Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
rlog
•
reset
3
votes
4
replies
519
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
9 weeks ago
Eva
▴ 10
3
votes
3
replies
1.2k
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 2.0 years ago by
Bioinformatics-414
• 0
3
votes
4
replies
2.0k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2
Normalization
rlog
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
dario.beraldi
• 0
1
vote
1
reply
1.0k
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
BT
▴ 10
1
vote
2
replies
1.3k
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.9 years ago
Bex
• 0
1
vote
3
replies
1.9k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
celiburgos
• 0
4
votes
4
replies
2.8k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 12 months ago by
Gordon Smyth
52k • written 3.0 years ago by
mohammedtoufiq91
▴ 10
6
votes
4
replies
1.9k
views
Which rlog should I use for DESeq2 analysis
samples
rlog
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
rafaelsolersanblas
▴ 50
2
votes
4
replies
3.4k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 2.9 years ago by
Sam
• 0 • written 3.2 years ago by
JB
▴ 10
1
vote
3
replies
3.1k
views
Different PCA results when using rlog and vst transformations
vsn
DESeq2
rlog
BatchEffect
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Diamond
• 0
1
vote
1
reply
1.1k
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
Fischer-philipp
▴ 30
8
votes
8
replies
1.5k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2
rlog
4.6 years ago
Zach Roe
▴ 10
1
vote
2
replies
1.0k
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 5.0 years ago by
Steve Lianoglou
★ 13k • written 5.0 years ago by
zhang.jianhai
▴ 10
0
votes
1
reply
3.4k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
juheon.maeng
• 0
1
vote
7
replies
1.4k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2
rlog
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
mschmidt
▴ 10
0
votes
3
replies
939
views
Normalisation upstream rlog
deseq2
rlog
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
zhang.jianhai
▴ 10
0
votes
15
replies
3.2k
views
rlog not found
rlog
rlog transformation
6.6 years ago
crowsreign42
• 0
0
votes
4
replies
2.3k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2
rlog
6.9 years ago
Frederik Ziebell
▴ 30
1
vote
2
replies
1.1k
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2
rlog
deseq
7.0 years ago
sreibe
• 0
0
votes
6
replies
3.7k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
7.2 years ago
lirongrossmann
▴ 80
0
votes
9
replies
2.1k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2
lfcshrink
rlog
7.3 years ago
pecot
• 0
2
votes
2
replies
3.0k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2
rlog
variancestabilizingtransformation
DESeq
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
Zach Roe
▴ 10
6
votes
4
replies
4.2k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 8.4 years ago by
Michael Love
43k • written 8.4 years ago by
longwoodSequencer
• 0
0
votes
3
replies
7.7k
views
What does DESeq2 rlog() return exactly?
deseq2
rlog
rlog transformation
8.8 years ago
lanhuong
▴ 20
3
votes
4
replies
2.3k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2
cummerbund
rlog
fpkm
clustering
8.9 years ago
Jon Bråte
▴ 260
2
votes
5
replies
2.9k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2
rlog
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
sjmonkley
▴ 40
4
votes
4
replies
2.5k
views
Dependence of rlog transformed value range on number of samples
deseq2
rlog
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
snsansom
▴ 20
0
votes
1
reply
3.3k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2
rlog
varianceStabilizingTransformation
lfproc
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
katja
• 0
28 results • Page
1 of 1
Recent ...
Replies
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
Just fit a model `~condition + experiment` where `condition` has three levels A, B and C. Ideally, use limma and include duplicate correlat…
Comment: Error in get_anno_data(ontology) : ontology not supported yet...
by
GODseeker
• 0
thank u so much ,god bless u,my dear friend.
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet...
by
Guido Hooiveld
★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Votes
A: Advice on correcting for batch effect using DESeq2
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
Awards
• All
Popular Question
to
martin.grigorov
▴ 10
Scholar
to
James W. MacDonald
67k
Popular Question
to
Benjamin
▴ 20
Popular Question
to
María Calvo
• 0
Popular Question
to
Gordon Smyth
52k
Locations
• All
India,
8 minutes ago
United States,
8 minutes ago
France,
9 minutes ago
The Netherlands,
14 minutes ago
United States,
23 minutes ago
Traffic: 1239 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6