Showing : rlog • reset
3
votes
3
replies
964
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 16 months ago by • 0
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
1
vote
1
reply
748
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.0k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
2.3 years ago Bex • 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
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.4 years ago by ▴ 10
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
2
votes
4
replies
2.5k
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
0
votes
3
replies
2.3k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
1
vote
1
reply
826
views
PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 3.2 years ago by 41k • written 3.2 years ago by ▴ 30
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
2
replies
799
views
Should the rlog normalised gene expression counts be further normalised?
rlog CPM RKPM
updated 4.4 years ago by ★ 13k • written 4.4 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
7
replies
1.2k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 4.8 years ago by 41k • written 4.8 years ago by ▴ 10
0
votes
3
replies
780
views
Normalisation upstream rlog
deseq2 rlog
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 10
0
votes
15
replies
2.7k
views
rlog not found
rlog rlog transformation
6.0 years ago crowsreign42 • 0
0
votes
4
replies
2.0k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2 rlog
6.2 years ago Frederik Ziebell ▴ 20
1
vote
2
replies
944
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
6.4 years ago sreibe • 0
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
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
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
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
0
votes
3
replies
7.3k
views
What does DESeq2 rlog() return exactly?
deseq2 rlog rlog transformation
8.1 years ago lanhuong ▴ 20
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
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
4
votes
4
replies
2.2k
views
Dependence of rlog transformed value range on number of samples
deseq2 rlog
updated 9.0 years ago by 41k • written 9.0 years ago by ▴ 20
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
27 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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