Showing : edaseq • reset
1
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4
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318
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 weeks ago samuel.channon • 0
2
votes
2
replies
277
views
between lane normalization upper quantile
EDASeq edgeR
9 weeks ago elesofi • 0
0
votes
1
reply
910
views
GC content
EDASeq
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
votes
6
replies
1.3k
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
3.3 years ago • updated 3.0 years ago gprezza • 0
1
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2
replies
966
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
3.5 years ago gprezza • 0
0
votes
0
replies
548
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
3.8 years ago abf ▴ 30
1
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1
reply
1.4k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 4.1 years ago by ★ 3.9k • written 4.1 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 4.4 years ago by 42k • written 4.4 years ago by • 0
4
votes
7
replies
1.6k
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
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1
reply
927
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Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 90
0
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3
replies
1.1k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.1 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 5.5 years ago by 42k • written 5.5 years ago by ▴ 30
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.5 years ago kbobowik • 0
1
vote
9
replies
2.7k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.7 years ago by ▴ 950 • written 5.7 years ago by ▴ 10
1
vote
1
reply
916
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
829
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
1.7k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 6.3 years ago by ★ 28k • written 6.4 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 6.5 years ago by ▴ 950 • written 6.5 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 6.5 years ago by ▴ 50 • written 6.5 years ago by ▴ 830
1
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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 8.0 years ago by ★ 13k • written 8.0 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 9.8 years ago by 42k • written 9.8 years ago by ★ 13k
2
votes
1
reply
2.0k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization EDASeq DESeq2 Normalization EDASeq DESeq2
updated 9.9 years ago by 42k • written 9.9 years ago by ★ 13k
0
votes
3
replies
2.6k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 10.6 years ago by ▴ 950 • written 10.6 years ago by ▴ 30
0
votes
1
reply
1.3k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 11.0 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 11.2 years ago by 50k • written 11.2 years ago by ▴ 90
0
votes
1
reply
1.5k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.3 years ago by ★ 6.5k • written 11.3 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
11.3 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 12.4 years ago by ▴ 500
35 results • Page 1 of 1
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Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
Hello everyone, I am new on this site but not a noob in R (I guess). I am facing the same problem. For me, it depends on the NOIseq plot fu…
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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