Showing : edaseq • reset
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329
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
7 months ago BioinfGuru ▴ 70
2
votes
3
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830
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
7 months ago BioinfGuru ▴ 70
1
vote
4
replies
856
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
12 months ago samuel.channon • 0
2
votes
2
replies
698
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between lane normalization upper quantile
EDASeq edgeR
12 months ago elesofi • 0
0
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1
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1.4k
views
GC content
EDASeq
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
2
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6
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1.7k
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.9 years ago Saulius ▴ 10
2
votes
2
replies
1.7k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.1 years ago • updated 3.8 years ago gprezza • 0
1
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2
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1.3k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.4 years ago gprezza • 0
0
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0
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706
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
4.7 years ago abf ▴ 30
1
vote
1
reply
1.9k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 4.9 years ago by ★ 4.0k • written 5.0 years ago by • 0
1
vote
6
replies
1.4k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
4
votes
7
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2.0k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.3 years ago by 52k • written 5.3 years ago by ▴ 60
1
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1
reply
1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 90
0
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3
replies
1.3k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
6.0 years ago jens • 0
1
vote
2
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1.6k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.2 years ago by ▴ 980 • written 6.2 years ago by ▴ 260
2
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3
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2.4k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
0
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0
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1.6k
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Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.4 years ago kbobowik • 0
1
vote
9
replies
3.2k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 6.5 years ago by ▴ 980 • written 6.5 years ago by ▴ 10
1
vote
1
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1.3k
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 6.8 years ago by ▴ 980 • written 6.8 years ago by ★ 1.6k
0
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1
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1.0k
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
6.8 years ago Dario Strbenac ★ 1.6k
2
votes
7
replies
26k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.9 years ago zoppoli pietro ▴ 10
0
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1
reply
2.0k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 130
2
votes
5
replies
2.9k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.3 years ago by ▴ 980 • written 7.4 years ago by • 0
6
votes
11
replies
3.8k
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 7.4 years ago by ▴ 50 • written 7.4 years ago by ▴ 840
1
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1
reply
1.8k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.4 years ago by ▴ 980 • written 7.4 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 8.8 years ago by ▴ 980 • written 8.8 years ago by • 0
2
votes
2
replies
3.5k
views
How is the mean-variance plot calculated?
edaseq
updated 8.9 years ago by ★ 13k • written 8.9 years ago by • 0
9
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7
replies
3.6k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 9.6 years ago by 52k • written 9.6 years ago by • 0
0
votes
4
replies
2.1k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 10.7 years ago by 43k • written 10.7 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 10.8 years ago by 43k • written 10.8 years ago by ★ 13k
0
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3
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2.9k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 11.5 years ago by ▴ 980 • written 11.5 years ago by ▴ 30
0
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1
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1.5k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 11.9 years ago by 52k • written 11.9 years ago by ▴ 40
0
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1
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2.2k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.0 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 12.0 years ago by 52k • written 12.1 years ago by ▴ 90
0
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1
reply
1.8k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.1 years ago by ★ 6.5k • written 12.1 years ago by 52k
0
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2
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2.2k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.1 years ago love ▴ 150
0
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4
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1.8k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 13.2 years ago by ▴ 980 • written 13.2 years ago by ▴ 500
37 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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