Showing : rlog • reset
0
votes
15
replies
2.7k
views
rlog not found
rlog rlog transformation
6.0 years ago crowsreign42 • 0
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
6.6 years ago pecot • 0
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
7
replies
1.2k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 10
0
votes
6
replies
3.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.6 years ago lirongrossmann ▴ 80
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 41k • written 8.6 years ago by ▴ 40
0
votes
4
replies
1.9k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2 rlog
6.2 years ago Frederik Ziebell ▴ 20
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 41k • written 2.1 years ago by • 0
4
votes
4
replies
2.2k
views
Dependence of rlog transformed value range on number of samples
deseq2 rlog
updated 8.9 years ago by 41k • written 8.9 years ago by ▴ 20
2
votes
4
replies
2.4k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 2.3 years ago by • 0 • written 2.5 years ago by ▴ 10
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
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 41k • written 7.7 years ago by • 0
6
votes
4
replies
1.5k
views
Which rlog should I use for DESeq2 analysis
samples rlog DESeq2
updated 2.4 years ago by 41k • written 2.4 years ago by ▴ 50
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
3
votes
3
replies
960
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 16 months ago by • 0
0
votes
3
replies
7.3k
views
What does DESeq2 rlog() return exactly?
deseq2 rlog rlog transformation
8.1 years ago lanhuong ▴ 20
0
votes
3
replies
779
views
Normalisation upstream rlog
deseq2 rlog
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
1
vote
3
replies
1.4k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
1
vote
2
replies
1.0k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
2.3 years ago Bex • 0
2
votes
2
replies
2.6k
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 41k • written 7.2 years ago by ▴ 10
1
vote
2
replies
940
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
6.4 years ago sreibe • 0
1
vote
2
replies
798
views
Should the rlog normalised gene expression counts be further normalised?
rlog CPM RKPM
updated 4.3 years ago by ★ 13k • written 4.3 years ago by ▴ 10
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 41k • written 9.0 years ago by • 0
1
vote
1
reply
742
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 2.2 years ago by 41k • written 2.3 years ago by ▴ 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 41k • written 4.5 years ago by • 0
1
vote
1
reply
821
views
PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 3.1 years ago by 41k • written 3.1 years ago by ▴ 30
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia) by christianhilton64 • 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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