Showing : EDAseq • reset
9
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7
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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
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
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
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
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
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
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
2
votes
2
replies
241
views
between lane normalization upper quantile
EDASeq edgeR
5 weeks ago elesofi • 0
2
votes
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
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
2
votes
7
replies
23k
views
use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.0 years ago zoppoli pietro ▴ 10
1
vote
1
reply
906
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
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
1
vote
4
replies
263
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
5 weeks ago • updated 4 weeks ago samuel.channon • 0
1
vote
1
reply
883
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 5.9 years ago by ▴ 950 • written 5.9 years ago by ★ 1.5k
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
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
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
937
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
3.4 years ago gprezza • 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
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
812
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
5.9 years ago Dario Strbenac ★ 1.5k
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
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
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
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
1.9k
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
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
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
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
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
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
0
votes
3
replies
1.0k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.0 years ago jens • 0
0
votes
0
replies
529
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
0
votes
1
reply
877
views
GC content
EDASeq
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
35 results • Page 1 of 1
Recent ...
Replies
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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