Showing : EDASeq • reset
2
votes
7
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23k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
5.9 years ago zoppoli pietro ▴ 10
2
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2
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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
6
votes
11
replies
2.9k
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
9
votes
7
replies
2.9k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 8.6 years ago by 50k • written 8.6 years ago by • 0
1
vote
9
replies
2.6k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.6 years ago by ▴ 950 • written 5.6 years ago by ▴ 10
0
votes
3
replies
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
votes
1
reply
2.5k
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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
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
2
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1
reply
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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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
11.0 years ago Kasper Daniel Hansen ★ 6.5k
0
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2
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1.8k
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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
replies
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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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
votes
1
reply
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
1
vote
2
replies
1.6k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 7.8 years ago by ▴ 950 • written 7.8 years ago by • 0
4
votes
7
replies
1.5k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 50
0
votes
4
replies
1.5k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 12.2 years ago by ▴ 950 • written 12.3 years ago by ▴ 500
0
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1
reply
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
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 6.4 years ago by ▴ 950 • written 6.4 years ago by ▴ 10
1
vote
1
reply
1.3k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
2
replies
1.3k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.3 years ago by ▴ 950 • written 5.3 years ago by ▴ 250
0
votes
1
reply
1.3k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 10.9 years ago by 50k • written 10.9 years ago by ▴ 40
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
2.9 years ago Saulius • 0
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.4 years ago kbobowik • 0
2
votes
2
replies
1.2k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
3.2 years ago • updated 2.9 years ago gprezza • 0
1
vote
6
replies
1.0k
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
0
votes
3
replies
1.0k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.0 years ago jens • 0
1
vote
2
replies
931
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
3.4 years ago gprezza • 0
1
vote
1
reply
896
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 90
1
vote
1
reply
877
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 5.8 years ago by ▴ 950 • written 5.8 years ago by ★ 1.5k
0
votes
1
reply
866
views
GC content
EDASeq
updated 21 months ago by ★ 4.0k • written 22 months ago by • 0
0
votes
1
reply
806
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
5.8 years ago Dario Strbenac ★ 1.5k
0
votes
0
replies
526
views
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
vote
4
replies
237
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
27 days ago • updated 26 days ago samuel.channon • 0
2
votes
2
replies
231
views
between lane normalization upper quantile
EDASeq edgeR
4 weeks ago • updated 29 days ago elesofi • 0
35 results • Page 1 of 1
Recent ...
Replies
Comment: flowStats Search Error by tholmes • 0
Thank you so much!
Comment: what is the sampleFiles by James W. MacDonald 65k
I don't see any sampleFiles argument for any function in that package. Ideally you would at least tell us what function you are using.
Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k
Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 700
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Votes
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
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