Showing : EDAseq • reset
1
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
5 weeks ago samuel.channon • 0
2
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2
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242
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between lane normalization upper quantile
EDASeq edgeR
5 weeks ago elesofi • 0
0
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1
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878
views
GC content
EDASeq
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
2
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6
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1.2k
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.0 years ago Saulius • 0
2
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2
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1.2k
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EDASeq normalization: genes with 0 counts
edgeR EDASeq
3.2 years ago • updated 2.9 years ago gprezza • 0
1
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2
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937
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
3.4 years ago gprezza • 0
0
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0
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529
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
3.7 years ago abf ▴ 30
1
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1
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1.4k
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EDASeq gene length normalization
edaseq r rna-seq
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
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6
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1.1k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
4
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7
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1.5k
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Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 4.4 years ago by 50k • written 4.4 years ago by ▴ 50
1
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1
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907
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Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 90
0
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3
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1.0k
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Possibly bug in newSeqExpressionSet function
software error EDASeq
5.0 years ago jens • 0
1
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2
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1.3k
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How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.3 years ago by ▴ 950 • written 5.3 years ago by ▴ 250
2
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3
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1.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 30
0
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0
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1.2k
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Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.4 years ago kbobowik • 0
1
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9
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2.6k
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EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.6 years ago by ▴ 950 • written 5.6 years ago by ▴ 10
1
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1
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884
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 5.9 years ago by ▴ 950 • written 5.9 years ago by ★ 1.5k
0
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1
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814
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
5.9 years ago Dario Strbenac ★ 1.5k
2
votes
7
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23k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.0 years ago zoppoli pietro ▴ 10
0
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1
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1.6k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 130
2
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5
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2.4k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 6.4 years ago by ▴ 950 • written 6.4 years ago by • 0
6
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11
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3.0k
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 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 830
1
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1
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1.5k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 6.5 years ago by ▴ 950 • written 6.5 years ago by ▴ 10
1
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2
replies
1.6k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 7.9 years ago by ▴ 950 • written 7.9 years ago by • 0
2
votes
2
replies
3.0k
views
How is the mean-variance plot calculated?
edaseq
updated 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
9
votes
7
replies
3.0k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
0
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4
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1.8k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 9.7 years ago by 41k • written 9.7 years ago by ★ 13k
2
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1
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1.9k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization EDASeq DESeq2 Normalization EDASeq DESeq2
updated 9.8 years ago by 41k • written 9.8 years ago by ★ 13k
0
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3
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2.5k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 10.5 years ago by ▴ 950 • written 10.5 years ago by ▴ 30
0
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1
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1.3k
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problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 10.9 years ago by 50k • written 10.9 years ago by ▴ 40
0
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1
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1.9k
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using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.1 years ago Kasper Daniel Hansen ★ 6.5k
0
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1
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2.5k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.1 years ago by 50k • written 11.1 years ago by ▴ 90
0
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1
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1.5k
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using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.2 years ago by ★ 6.5k • written 11.2 years ago by 50k
0
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2
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1.8k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.2 years ago love ▴ 150
0
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4
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1.5k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 12.3 years ago by ▴ 950 • written 12.3 years ago by ▴ 500
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
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…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
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?
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