Showing : rlog • reset
3
votes
4
replies
863
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
6 months ago Eva ▴ 10
3
votes
3
replies
1.3k
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 2.4 years ago by • 0
3
votes
4
replies
2.3k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
vote
1
reply
1.1k
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
1
vote
2
replies
1.5k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
3.3 years ago Bex • 0
1
vote
3
replies
2.1k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
4
votes
4
replies
3.2k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 17 months ago by 52k • written 3.4 years ago by ▴ 10
6
votes
4
replies
2.1k
views
Which rlog should I use for DESeq2 analysis
samples rlog DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 50
2
votes
4
replies
3.9k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 3.3 years ago by • 0 • written 3.5 years ago by ▴ 10
1
vote
3
replies
3.5k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
1
reply
1.2k
views
PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 30
8
votes
8
replies
1.8k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2 rlog
5.0 years ago Zach Roe ▴ 10
1
vote
2
replies
1.1k
views
Should the rlog normalised gene expression counts be further normalised?
rlog CPM RKPM
updated 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 10
0
votes
1
reply
3.9k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
7
replies
1.6k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
3
replies
1.0k
views
Normalisation upstream rlog
deseq2 rlog
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
0
votes
15
replies
3.4k
views
rlog not found
rlog rlog transformation
7.0 years ago crowsreign42 • 0
0
votes
4
replies
2.5k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2 rlog
7.2 years ago Frederik Ziebell ▴ 30
1
vote
2
replies
1.2k
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
7.4 years ago sreibe • 0
0
votes
6
replies
3.9k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
7.6 years ago lirongrossmann ▴ 80
0
votes
9
replies
2.3k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2 lfcshrink rlog
7.6 years ago pecot • 0
2
votes
2
replies
3.2k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2 rlog variancestabilizingtransformation DESeq
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
6
votes
4
replies
4.4k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
0
votes
3
replies
7.8k
views
What does DESeq2 rlog() return exactly?
deseq2 rlog rlog transformation
9.1 years ago lanhuong ▴ 20
3
votes
4
replies
2.4k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
9.3 years ago Jon Bråte ▴ 260
2
votes
5
replies
3.1k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2 rlog
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 40
4
votes
4
replies
2.6k
views
Dependence of rlog transformed value range on number of samples
deseq2 rlog
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 20
0
votes
1
reply
3.4k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2 rlog varianceStabilizingTransformation lfproc
updated 10.0 years ago by 43k • written 10.0 years ago by • 0
28 results • Page 1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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