Showing : rlog • reset
3
votes
3
replies
385
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 5 months ago by • 0
3
votes
4
replies
866
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 14 months ago by 40k • written 14 months ago by • 0
1
vote
1
reply
441
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 16 months ago by 40k • written 16 months ago by ▴ 10
1
vote
2
replies
572
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
16 months ago Bex • 0
1
vote
3
replies
856
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 16 months ago by 40k • written 16 months ago by • 0
3
votes
3
replies
910
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
written 17 months ago by ▴ 10
6
votes
4
replies
1.0k
views
Which rlog should I use for DESeq2 analysis
samples rlog DESeq2
updated 18 months ago by 40k • written 18 months ago by ▴ 50
2
votes
4
replies
1.3k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 16 months ago by • 0 • written 19 months ago by ▴ 10
0
votes
3
replies
1.3k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 21 months ago by 40k • written 21 months ago by • 0
1
vote
1
reply
517
views
PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 2.3 years ago by 40k • written 2.3 years ago by ▴ 30
8
votes
8
replies
788
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2 rlog
3.1 years ago Zach Roe ▴ 10
1
vote
2
replies
515
views
Should the rlog normalised gene expression counts be further normalised?
rlog CPM RKPM
updated 3.5 years ago by 13k • written 3.5 years ago by ▴ 10
0
votes
1
reply
1.9k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 3.6 years ago by 40k • written 3.6 years ago by • 0
1
vote
7
replies
871
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 3.9 years ago by 40k • written 3.9 years ago by ▴ 10
0
votes
3
replies
548
views
Normalisation upstream rlog
deseq2 rlog
updated 4.2 years ago by 40k • written 4.2 years ago by ▴ 10
0
votes
15
replies
2.0k
views
rlog not found
rlog rlog transformation
5.1 years ago crowsreign42 • 0
0
votes
4
replies
1.4k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2 rlog
5.4 years ago • updated 5.3 years ago Frederik Ziebell ▴ 10
1
vote
2
replies
685
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
5.5 years ago sreibe • 0
0
votes
6
replies
2.3k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
5.7 years ago lirongrossmann ▴ 80
0
votes
9
replies
1.3k
views
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2 lfcshrink rlog
5.7 years ago pecot • 0
2
votes
2
replies
2.3k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2 rlog variancestabilizingtransformation DESeq
updated 6.3 years ago by 40k • written 6.3 years ago by ▴ 10
6
votes
4
replies
3.1k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 6.8 years ago by 40k • written 6.8 years ago by • 0
0
votes
3
replies
6.7k
views
What does DESeq2 rlog() return exactly?
deseq2 rlog rlog transformation
7.2 years ago lanhuong ▴ 20
3
votes
4
replies
1.6k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
7.4 years ago Jon Bråte ▴ 250
2
votes
5
replies
2.3k
views
Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
DESeq2 rlog
updated 7.7 years ago by 40k • written 7.7 years ago by ▴ 40
4
votes
4
replies
1.8k
views
Dependence of rlog transformed value range on number of samples
deseq2 rlog
updated 8.1 years ago by 40k • written 8.1 years ago by ▴ 20
0
votes
1
reply
2.2k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2 rlog varianceStabilizingTransformation lfproc
updated 8.1 years ago by 40k • written 8.1 years ago by • 0
27 results • Page 1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind by Chris • 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind by Chris • 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting by phelankj • 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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