Showing : EDASeq • reset
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295
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
5 months ago BioinfGuru ▴ 70
2
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3
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633
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
1
vote
4
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735
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
10 months ago samuel.channon • 0
2
votes
2
replies
615
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between lane normalization upper quantile
EDASeq edgeR
10 months ago elesofi • 0
0
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1
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1.3k
views
GC content
EDASeq
updated 2.6 years ago by ★ 4.6k • written 2.6 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
3.7 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
1.2k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.2 years ago gprezza • 0
0
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0
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683
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
4.5 years ago abf ▴ 30
1
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1
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1.7k
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EDASeq gene length normalization
edaseq r rna-seq
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
vote
6
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1.3k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
4
votes
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 5.1 years ago by 52k • written 5.1 years ago by ▴ 50
1
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1
reply
1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 90
0
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3
replies
1.3k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.8 years ago jens • 0
1
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2
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1.5k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.0 years ago by ▴ 980 • written 6.0 years ago by ▴ 260
2
votes
3
replies
2.2k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.2 years ago by 43k • written 6.2 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
6.2 years ago kbobowik • 0
1
vote
9
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3.1k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 6.3 years ago by ▴ 980 • written 6.3 years ago by ▴ 10
1
vote
1
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1.2k
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 6.6 years ago by ▴ 980 • written 6.6 years ago by ★ 1.5k
0
votes
1
reply
968
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
6.6 years ago Dario Strbenac ★ 1.5k
2
votes
7
replies
25k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.7 years ago zoppoli pietro ▴ 10
0
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1
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1.9k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 130
2
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5
replies
2.8k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.2 years ago by ▴ 980 • written 7.2 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 7.2 years ago by ▴ 50 • written 7.2 years ago by ▴ 840
1
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1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.2 years ago by ▴ 980 • written 7.2 years ago by ▴ 10
1
vote
2
replies
1.8k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 8.6 years ago by ▴ 980 • written 8.6 years ago by • 0
2
votes
2
replies
3.4k
views
How is the mean-variance plot calculated?
edaseq
updated 8.7 years ago by ★ 13k • written 8.7 years ago by • 0
9
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7
replies
3.4k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 9.4 years ago by 52k • written 9.4 years ago by • 0
0
votes
4
replies
2.1k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 10.5 years ago by 43k • written 10.5 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 10.6 years ago by 43k • written 10.6 years ago by ★ 13k
0
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3
replies
2.9k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 11.3 years ago by ▴ 980 • written 11.3 years ago by ▴ 30
0
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1
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1.4k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 11.7 years ago by 52k • written 11.7 years ago by ▴ 40
0
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1
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2.1k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.8 years ago Kasper Daniel Hansen ★ 6.5k
0
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1
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2.8k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.9 years ago by 52k • written 11.9 years ago by ▴ 90
0
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1
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1.7k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.9 years ago by ★ 6.5k • written 11.9 years ago by 52k
0
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2
replies
2.1k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.0 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 13.0 years ago by ▴ 980 • written 13.1 years ago by ▴ 500
37 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
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