Showing : EDASeq • reset
0
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490
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
15 months ago BioinfGuru ▴ 70
2
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3
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1.3k
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
15 months ago BioinfGuru ▴ 70
1
vote
4
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1.1k
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
20 months ago samuel.channon • 0
2
votes
2
replies
938
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between lane normalization upper quantile
EDASeq edgeR
20 months ago elesofi • 0
0
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1
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1.6k
views
GC content
EDASeq
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
2
votes
6
replies
1.9k
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
4.5 years ago Saulius ▴ 10
2
votes
2
replies
1.9k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.7 years ago • updated 4.4 years ago gprezza • 0
1
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2
replies
1.5k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
5.0 years ago gprezza • 0
0
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0
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835
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5.3 years ago abf ▴ 30
1
vote
1
reply
2.2k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 5.5 years ago by ★ 4.0k • written 5.6 years ago by • 0
1
vote
6
replies
1.6k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
4
votes
7
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2.3k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 60
1
vote
1
reply
1.3k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 100
0
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3
replies
1.6k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
6.6 years ago jens • 0
1
vote
2
replies
1.7k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.8 years ago by ▴ 980 • written 6.8 years ago by ▴ 270
2
votes
3
replies
2.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 30
0
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0
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1.7k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
7.0 years ago kbobowik • 0
1
vote
9
replies
3.6k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 7.1 years ago by ▴ 980 • written 7.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 7.4 years ago by ▴ 980 • written 7.4 years ago by ★ 1.6k
0
votes
1
reply
1.1k
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
7.4 years ago Dario Strbenac ★ 1.6k
2
votes
7
replies
26k
views
use EDAseq normalized data as input of DESeq2
deseq2 edaseq
7.5 years ago zoppoli pietro ▴ 10
0
votes
1
reply
2.2k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 130
2
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5
replies
3.2k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.9 years ago by ▴ 980 • written 8.0 years ago by • 0
6
votes
11
replies
4.2k
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 8.0 years ago by ▴ 50 • written 8.0 years ago by ▴ 840
1
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1
reply
2.0k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 8.0 years ago by ▴ 980 • written 8.0 years ago by ▴ 10
1
vote
2
replies
2.0k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 9.4 years ago by ▴ 980 • written 9.4 years ago by • 0
2
votes
2
replies
3.7k
views
How is the mean-variance plot calculated?
edaseq
updated 9.5 years ago by ★ 13k • written 9.5 years ago by • 0
9
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7
replies
3.9k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
0
votes
4
replies
2.3k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 11.3 years ago by 43k • written 11.3 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 11.4 years ago by 43k • written 11.4 years ago by ★ 13k
0
votes
3
replies
3.1k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 12.1 years ago by ▴ 980 • written 12.1 years ago by ▴ 30
0
votes
1
reply
1.6k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 12.5 years ago by 53k • written 12.5 years ago by ▴ 40
0
votes
1
reply
2.4k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.6 years ago Kasper Daniel Hansen ★ 6.5k
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 12.6 years ago by 53k • written 12.7 years ago by ▴ 90
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.7 years ago by ★ 6.5k • written 12.7 years ago by 53k
0
votes
2
replies
2.4k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.7 years ago love ▴ 150
0
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4
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2.0k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 13.8 years ago by ▴ 980 • written 13.8 years ago by ▴ 500
37 results • Page 1 of 1
Recent ...
Replies
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
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Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Votes
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
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