Showing : rlog • reset
3
votes
4
replies
1.2k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
12 months ago Eva ▴ 10
3
votes
3
replies
1.4k
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 2.8 years ago by • 0
3
votes
4
replies
2.4k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
vote
1
reply
1.2k
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
1
vote
2
replies
1.6k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
3.7 years ago Bex • 0
1
vote
3
replies
2.3k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
4
votes
4
replies
3.4k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 22 months ago by 53k • written 3.8 years ago by ▴ 10
6
votes
4
replies
2.2k
views
Which rlog should I use for DESeq2 analysis
samples rlog DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 50
2
votes
4
replies
4.3k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 3.7 years ago by • 0 • written 4.0 years ago by ▴ 10
1
vote
3
replies
3.8k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
1
vote
1
reply
1.3k
views
PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 30
8
votes
8
replies
1.9k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2 rlog
5.4 years ago Zach Roe ▴ 10
1
vote
2
replies
1.2k
views
Should the rlog normalised gene expression counts be further normalised?
rlog CPM RKPM
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 10
0
votes
1
reply
4.2k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
vote
7
replies
1.9k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Normalisation upstream rlog
deseq2 rlog
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
15
replies
3.7k
views
rlog not found
rlog rlog transformation
7.4 years ago crowsreign42 • 0
0
votes
4
replies
2.6k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2 rlog
7.7 years ago Frederik Ziebell ▴ 30
1
vote
2
replies
1.4k
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
7.8 years ago sreibe • 0
0
votes
6
replies
4.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
8.0 years ago lirongrossmann ▴ 80
0
votes
9
replies
2.5k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2 lfcshrink rlog
8.1 years ago pecot • 0
2
votes
2
replies
3.3k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2 rlog variancestabilizingtransformation DESeq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
6
votes
4
replies
4.6k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
0
votes
3
replies
8.0k
views
What does DESeq2 rlog() return exactly?
deseq2 rlog rlog transformation
9.6 years ago lanhuong ▴ 20
3
votes
4
replies
2.5k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
9.7 years ago Jon Bråte ▴ 270
2
votes
5
replies
3.2k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2 rlog
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 40
4
votes
4
replies
2.7k
views
Dependence of rlog transformed value range on number of samples
deseq2 rlog
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 20
0
votes
1
reply
3.5k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2 rlog varianceStabilizingTransformation lfproc
updated 10.5 years ago by 43k • written 10.5 years ago by • 0
28 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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