Showing : EDAseq • reset
0
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256
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
3 months ago BioinfGuru ▴ 70
2
votes
3
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499
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
3 months ago BioinfGuru ▴ 70
1
vote
4
replies
646
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 months ago samuel.channon • 0
2
votes
2
replies
538
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between lane normalization upper quantile
EDASeq edgeR
8 months ago elesofi • 0
0
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1
reply
1.2k
views
GC content
EDASeq
updated 2.4 years ago by ★ 4.5k • written 2.4 years ago by • 0
2
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6
replies
1.5k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.6 years ago • updated 3.5 years ago Saulius ▴ 10
2
votes
2
replies
1.5k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
3.8 years ago • updated 3.5 years ago gprezza • 0
1
vote
2
replies
1.2k
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.0 years ago gprezza • 0
0
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0
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657
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
4.3 years ago abf ▴ 30
1
vote
1
reply
1.7k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 4.6 years ago by ★ 4.0k • written 4.6 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 4.9 years ago by 43k • written 4.9 years ago by • 0
4
votes
7
replies
1.8k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 4.9 years ago by 51k • written 4.9 years ago by ▴ 50
1
vote
1
reply
1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 90
0
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3
replies
1.2k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
5.6 years ago jens • 0
1
vote
2
replies
1.5k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.9 years ago by ▴ 980 • written 5.9 years ago by ▴ 260
2
votes
3
replies
2.1k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
0
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0
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1.4k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.0 years ago kbobowik • 0
1
vote
9
replies
3.0k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 6.2 years ago by ▴ 980 • written 6.2 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 6.4 years ago by ▴ 980 • written 6.4 years ago by ★ 1.5k
0
votes
1
reply
941
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
6.4 years ago Dario Strbenac ★ 1.5k
2
votes
7
replies
24k
views
use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.6 years ago zoppoli pietro ▴ 10
0
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1
reply
1.9k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 130
2
votes
5
replies
2.7k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.0 years ago by ▴ 980 • written 7.0 years ago by • 0
6
votes
11
replies
3.5k
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 7.0 years ago by ▴ 50 • written 7.0 years ago by ▴ 840
1
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1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.1 years ago by ▴ 980 • written 7.1 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 8.5 years ago by ▴ 980 • written 8.5 years ago by • 0
2
votes
2
replies
3.3k
views
How is the mean-variance plot calculated?
edaseq
updated 8.5 years ago by ★ 13k • written 8.5 years ago by • 0
9
votes
7
replies
3.3k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 9.3 years ago by 51k • written 9.3 years ago by • 0
0
votes
4
replies
2.0k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 10.3 years ago by 43k • written 10.3 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 10.4 years ago by 43k • written 10.4 years ago by ★ 13k
0
votes
3
replies
2.8k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 11.1 years ago by ▴ 980 • written 11.1 years ago by ▴ 30
0
votes
1
reply
1.4k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 11.5 years ago by 51k • written 11.5 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
11.7 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
1
reply
2.7k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.7 years ago by 51k • written 11.7 years ago by ▴ 90
0
votes
1
reply
1.7k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.8 years ago by ★ 6.5k • written 11.8 years ago by 51k
0
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2
replies
2.1k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.8 years ago love ▴ 150
0
votes
4
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1.7k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 12.8 years ago by ▴ 980 • written 12.9 years ago by ▴ 500
37 results • Page 1 of 1
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Comment: Struggle with the replicates of epic array data by Melisa Tecik • 0
Thanks you so much for the instructions. I also tried M values as you suggested but sadly the result was the same. Apparently, the problem …
Answer: bioconductor packages on bioconda by James W. MacDonald 67k
The bioconda people are responsible for bioconda, so you should ask them if/when they are going to update.
Answer: txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome by James W. MacDonald 67k
The default for `plotKaryotype` is to use hg19.
Comment: Is it possible to parallelise saveHDF5SummarizedExperiment by Stefano Mangiola ▴ 20
saveTileDBSummarizedExperiment would be awesome. I think we need performance for execution time and memory required to save.
Comment: Create Illmina bead summary data by Liu • 0
Hi! Yes, thank you! I completely agree. I am just curious about how these two files are processed with AVG_Gre and detection p-value. I am …
Votes
Answer: Struggle with the replicates of epic array data
Answer: bioconductor packages on bioconda
Appropriate use of the function treat of the limma package
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
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Scholar to James W. MacDonald 67k
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