Showing : edaseq • reset
0
votes
0
replies
295
views
Are equal whisker lengths important in an RLE plot?
EDASeq EDA
5 months ago BioinfGuru ▴ 70
2
votes
3
replies
622
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
1
vote
4
replies
729
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
611
views
between lane normalization upper quantile
EDASeq edgeR
10 months ago elesofi • 0
0
votes
1
reply
1.3k
views
GC content
EDASeq
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
2
votes
6
replies
1.6k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.7 years ago Saulius ▴ 10
2
votes
2
replies
1.6k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
3.9 years ago • updated 3.6 years ago gprezza • 0
1
vote
2
replies
1.2k
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.2 years ago gprezza • 0
0
votes
0
replies
680
views
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
vote
1
reply
1.7k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 4.7 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
vote
6
replies
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
replies
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
vote
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
votes
3
replies
1.3k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.8 years ago jens • 0
1
vote
2
replies
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
votes
0
replies
1.5k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.2 years ago kbobowik • 0
1
vote
9
replies
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
reply
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
967
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
6.6 years ago Dario Strbenac ★ 1.5k
2
votes
7
replies
25k
views
use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.7 years ago zoppoli pietro ▴ 10
0
votes
1
reply
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
votes
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
3.6k
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
vote
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
votes
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
votes
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
votes
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
votes
1
reply
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
votes
1
reply
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
votes
1
reply
2.8k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.8 years ago by 52k • written 11.9 years ago by ▴ 90
0
votes
1
reply
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
votes
2
replies
2.1k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.9 years ago love ▴ 150
0
votes
4
replies
1.8k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 13.0 years ago by ▴ 980 • written 13.0 years ago by ▴ 500
37 results • Page 1 of 1
Recent ...
Replies
Answer: WGCNA sample-data preprocessing order by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. …
Answer: WGCNA: Can we use high power (26) for signed network? by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. C…
Answer: Ph.D. scholar by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. C…
Comment: Recount3 data correspond to TCGA data by Fep29 • 0
Hi, This the solution to mapping TCGA ids in Recount3 to the ids used in the TCGA barcodes: library(recount3) human_projects <- …
Answer: Unable to find sample sheet file for ChAMP methylation data analysis by James W. MacDonald 67k
There is an example file in the extdata directory of the `minfiData` package that you could emulate.
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Martin Morgan 25k
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Joseph Fass ▴ 70
Popular Question to Peter Hickey ▴ 750
Locations • All
The Netherlands, 26 minutes ago
EMBL Heidelberg, 50 minutes ago
India, 58 minutes ago
United States, 1 hour ago
Germany, 1 hour ago
Traffic: 787 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6