Showing : EDASeq • reset
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318
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
6 months ago BioinfGuru ▴ 70
2
votes
3
replies
730
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
6 months ago BioinfGuru ▴ 70
1
vote
4
replies
789
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
11 months ago samuel.channon • 0
2
votes
2
replies
658
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between lane normalization upper quantile
EDASeq edgeR
11 months ago elesofi • 0
0
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1
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1.3k
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GC content
EDASeq
updated 2.7 years ago by ★ 4.7k • written 2.7 years ago by • 0
2
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6
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1.6k
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.8 years ago Saulius ▴ 10
2
votes
2
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1.6k
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EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.0 years ago • updated 3.7 years ago gprezza • 0
1
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2
replies
1.3k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.3 years ago gprezza • 0
0
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0
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697
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
4.6 years ago abf ▴ 30
1
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1
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1.8k
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EDASeq gene length normalization
edaseq r rna-seq
updated 4.8 years ago by ★ 4.0k • written 4.9 years ago by • 0
1
vote
6
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1.4k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
4
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7
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1.9k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.2 years ago by 52k • written 5.2 years ago by ▴ 50
1
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1
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1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 90
0
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3
replies
1.3k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.9 years ago jens • 0
1
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2
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1.6k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.1 years ago by ▴ 980 • written 6.1 years ago by ▴ 260
2
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3
replies
2.3k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
0
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0
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1.5k
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Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.3 years ago kbobowik • 0
1
vote
9
replies
3.2k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 6.4 years ago by ▴ 980 • written 6.4 years ago by ▴ 10
1
vote
1
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1.2k
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Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 6.7 years ago by ▴ 980 • written 6.7 years ago by ★ 1.6k
0
votes
1
reply
990
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
6.7 years ago Dario Strbenac ★ 1.6k
2
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7
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25k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.8 years ago zoppoli pietro ▴ 10
0
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1
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2.0k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 130
2
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5
replies
2.9k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by • 0
6
votes
11
replies
3.7k
views
Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
tcgabiolinks rnaseq normalization EDASeq
updated 7.3 years ago by ▴ 50 • written 7.3 years ago by ▴ 840
1
vote
1
reply
1.8k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by ▴ 10
1
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2
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1.8k
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Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 8.7 years ago by ▴ 980 • written 8.7 years ago by • 0
2
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2
replies
3.4k
views
How is the mean-variance plot calculated?
edaseq
updated 8.8 years ago by ★ 13k • written 8.8 years ago by • 0
9
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7
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3.5k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 9.5 years ago by 52k • written 9.5 years ago by • 0
0
votes
4
replies
2.1k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 10.6 years ago by 43k • written 10.6 years ago by ★ 13k
2
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1
reply
2.1k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization EDASeq DESeq2 Normalization EDASeq DESeq2
updated 10.7 years ago by 43k • written 10.7 years ago by ★ 13k
0
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3
replies
2.9k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 11.4 years ago by ▴ 980 • written 11.4 years ago by ▴ 30
0
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1
reply
1.5k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 11.8 years ago by 52k • written 11.8 years ago by ▴ 40
0
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1
reply
2.2k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.9 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
1
reply
2.8k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 12.0 years ago by 52k • written 12.0 years ago by ▴ 90
0
votes
1
reply
1.7k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.0 years ago by ★ 6.5k • written 12.0 years ago by 52k
0
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2
replies
2.2k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.1 years ago love ▴ 150
0
votes
4
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1.8k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 13.1 years ago by ▴ 980 • written 13.2 years ago by ▴ 500
37 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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