Showing : EDAseq • reset
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443
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
12 months ago BioinfGuru ▴ 70
2
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3
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1.1k
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
12 months ago BioinfGuru ▴ 70
1
vote
4
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1.0k
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
17 months ago samuel.channon • 0
2
votes
2
replies
857
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between lane normalization upper quantile
EDASeq edgeR
17 months ago elesofi • 0
0
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1
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1.5k
views
GC content
EDASeq
updated 3.2 years ago by ★ 4.9k • written 3.2 years ago by • 0
2
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6
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1.9k
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
4.3 years ago Saulius ▴ 10
2
votes
2
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1.8k
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EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.6 years ago • updated 4.3 years ago gprezza • 0
1
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2
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1.5k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.8 years ago gprezza • 0
0
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0
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788
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5.1 years ago abf ▴ 30
1
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1
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2.1k
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EDASeq gene length normalization
edaseq r rna-seq
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
1
vote
6
replies
1.5k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
4
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7
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2.2k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.7 years ago by 52k • written 5.7 years ago by ▴ 60
1
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1
reply
1.2k
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Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 100
0
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3
replies
1.5k
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Possibly bug in newSeqExpressionSet function
software error EDASeq
6.4 years ago jens • 0
1
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2
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1.7k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.6 years ago by ▴ 980 • written 6.6 years ago by ▴ 270
2
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3
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2.6k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
0
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0
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1.7k
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Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.8 years ago kbobowik • 0
1
vote
9
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3.5k
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EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 6.9 years ago by ▴ 980 • written 6.9 years ago by ▴ 10
1
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1
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1.4k
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Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 7.2 years ago by ▴ 980 • written 7.2 years ago by ★ 1.6k
0
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1
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1.1k
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meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
7.2 years ago Dario Strbenac ★ 1.6k
2
votes
7
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26k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
7.3 years ago zoppoli pietro ▴ 10
0
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1
reply
2.2k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 130
2
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5
replies
3.1k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.8 years ago by ▴ 980 • written 7.8 years ago by • 0
6
votes
11
replies
4.1k
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 7.8 years ago by ▴ 50 • written 7.8 years ago by ▴ 840
1
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1
reply
2.0k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.8 years ago by ▴ 980 • written 7.8 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 9.2 years ago by ▴ 980 • written 9.2 years ago by • 0
2
votes
2
replies
3.6k
views
How is the mean-variance plot calculated?
edaseq
updated 9.3 years ago by ★ 13k • written 9.3 years ago by • 0
9
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7
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3.8k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 10.0 years ago by 52k • written 10.0 years ago by • 0
0
votes
4
replies
2.2k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 11.1 years ago by 43k • written 11.1 years ago by ★ 13k
2
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1
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2.2k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization EDASeq DESeq2 Normalization EDASeq DESeq2
updated 11.2 years ago by 43k • written 11.2 years ago by ★ 13k
0
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3
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3.1k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 11.9 years ago by ▴ 980 • written 11.9 years ago by ▴ 30
0
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1
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1.5k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 12.3 years ago by 52k • written 12.3 years ago by ▴ 40
0
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1
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2.3k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.4 years ago Kasper Daniel Hansen ★ 6.5k
0
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1
reply
2.9k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 12.5 years ago by 52k • written 12.5 years ago by ▴ 90
0
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1
reply
1.8k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.5 years ago by ★ 6.5k • written 12.5 years ago by 52k
0
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2
replies
2.3k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.6 years ago love ▴ 150
0
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4
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1.9k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 13.6 years ago by ▴ 980 • written 13.7 years ago by ▴ 500
37 results • Page 1 of 1
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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