Showing : EDAseq • reset
2
votes
7
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26k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
7.7 years ago zoppoli pietro ▴ 10
6
votes
11
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4.4k
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 8.1 years ago by ▴ 50 • written 8.2 years ago by ▴ 840
9
votes
7
replies
4.0k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 10.4 years ago by 53k • written 10.4 years ago by • 0
2
votes
2
replies
3.8k
views
How is the mean-variance plot calculated?
edaseq
updated 9.7 years ago by ★ 13k • written 9.7 years ago by • 0
1
vote
9
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3.7k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by ▴ 10
0
votes
3
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3.2k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 12.3 years ago by ▴ 980 • written 12.3 years ago by ▴ 30
2
votes
5
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3.2k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 8.1 years ago by ▴ 980 • written 8.1 years ago by • 0
0
votes
1
reply
3.0k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 12.8 years ago by 53k • written 12.8 years ago by ▴ 90
2
votes
3
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2.8k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 30
0
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2
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2.5k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.9 years ago love ▴ 150
4
votes
7
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2.4k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 60
0
votes
1
reply
2.4k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.8 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
4
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2.4k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 11.4 years ago by 43k • written 11.4 years ago by ★ 13k
2
votes
1
reply
2.3k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization EDASeq DESeq2 Normalization EDASeq DESeq2
updated 11.6 years ago by 43k • written 11.6 years ago by ★ 13k
0
votes
1
reply
2.3k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 130
1
vote
1
reply
2.2k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
vote
2
replies
2.1k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 9.6 years ago by ▴ 980 • written 9.6 years ago by • 0
1
vote
1
reply
2.0k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 8.2 years ago by ▴ 980 • written 8.2 years ago by ▴ 10
0
votes
4
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2.0k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 14.0 years ago by ▴ 980 • written 14.0 years ago by ▴ 500
2
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6
replies
2.0k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
4.7 years ago Saulius ▴ 10
2
votes
2
replies
2.0k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.9 years ago • updated 4.6 years ago gprezza • 0
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.9 years ago by ★ 6.5k • written 12.9 years ago by 53k
1
vote
2
replies
1.8k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 7.0 years ago by ▴ 980 • written 7.0 years ago by ▴ 270
0
votes
0
replies
1.8k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
7.1 years ago kbobowik • 0
1
vote
6
replies
1.7k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
1.7k
views
GC content
EDASeq
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
votes
3
replies
1.6k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
6.8 years ago jens • 0
0
votes
1
reply
1.6k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 12.7 years ago by 53k • written 12.7 years ago by ▴ 40
1
vote
2
replies
1.6k
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
5.1 years ago gprezza • 0
1
vote
1
reply
1.5k
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 7.6 years ago by ▴ 980 • written 7.6 years ago by ★ 1.6k
2
votes
3
replies
1.4k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
17 months ago BioinfGuru ▴ 70
1
vote
1
reply
1.3k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 100
1
vote
4
replies
1.2k
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
22 months ago samuel.channon • 0
0
votes
1
reply
1.2k
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
7.6 years ago Dario Strbenac ★ 1.6k
2
votes
2
replies
1000
views
between lane normalization upper quantile
EDASeq edgeR
22 months ago elesofi • 0
0
votes
0
replies
883
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5.5 years ago abf ▴ 30
0
votes
0
replies
523
views
Are equal whisker lengths important in an RLE plot?
EDASeq EDA
17 months ago BioinfGuru ▴ 70
37 results • Page 1 of 1
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
Awards • All
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
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