Showing : EDAseq • reset
1
vote
4
replies
266
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
5 weeks ago samuel.channon • 0
2
votes
2
replies
245
views
between lane normalization upper quantile
EDASeq edgeR
6 weeks ago • updated 5 weeks ago elesofi • 0
0
votes
1
reply
880
views
GC content
EDASeq
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.0 years ago Saulius • 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
2
replies
941
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
3.4 years ago gprezza • 0
0
votes
0
replies
530
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
1
reply
1.4k
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
6
replies
1.1k
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
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 4.4 years ago by 50k • written 4.4 years ago by ▴ 50
1
vote
1
reply
909
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 90
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
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
2
votes
3
replies
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
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.4 years ago kbobowik • 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
1
vote
1
reply
887
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 5.9 years ago by ▴ 950 • written 5.9 years ago by ★ 1.5k
0
votes
1
reply
816
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
5.9 years ago Dario Strbenac ★ 1.5k
2
votes
7
replies
23k
views
use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.0 years ago zoppoli pietro ▴ 10
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
2
votes
5
replies
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
6
votes
11
replies
3.0k
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
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 6.5 years ago by ▴ 950 • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 7.9 years ago by ▴ 950 • written 7.9 years ago by • 0
2
votes
2
replies
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
9
votes
7
replies
3.0k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
0
votes
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
votes
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
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
1.3k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 10.9 years ago by 50k • written 11.0 years ago by ▴ 40
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.1 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
1
reply
2.5k
views
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
0
votes
1
reply
1.5k
views
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
0
votes
2
replies
1.8k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.2 years ago love ▴ 150
0
votes
4
replies
1.5k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 12.3 years ago by ▴ 950 • written 12.3 years ago by ▴ 500
35 results • Page 1 of 1
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
India, 19 minutes ago
South Korea, 25 minutes ago
France, 36 minutes ago
INDIA, 1 hour ago
United States, 1 hour ago
Traffic: 678 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