Showing : EDAseq • reset
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 7.3 years ago by ▴ 50 • written 7.4 years ago by ▴ 840
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
2
votes
7
replies
25k
views
use EDAseq normalized data as input of DESeq2
deseq2 edaseq
6.9 years ago zoppoli pietro ▴ 10
9
votes
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
4
votes
7
replies
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 ▴ 50
2
votes
6
replies
1.7k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.9 years ago Saulius ▴ 10
1
vote
6
replies
1.4k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
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 7.3 years ago by • 0
1
vote
4
replies
829
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
12 months ago samuel.channon • 0
0
votes
4
replies
2.1k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 10.6 years ago by 43k • written 10.6 years ago by ★ 13k
0
votes
4
replies
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
2
votes
3
replies
802
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
7 months ago BioinfGuru ▴ 70
0
votes
3
replies
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
votes
3
replies
1.3k
views
Possibly bug in newSeqExpressionSet function
software error EDASeq
6.0 years ago jens • 0
2
votes
3
replies
2.4k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
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
2
votes
2
replies
690
views
between lane normalization upper quantile
EDASeq edgeR
12 months ago elesofi • 0
1
vote
2
replies
1.3k
views
Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.3 years ago gprezza • 0
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
vote
2
replies
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
0
votes
2
replies
2.2k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.1 years ago love ▴ 150
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
1
vote
1
reply
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
votes
1
reply
1.7k
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
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 12.0 years ago by ▴ 90
0
votes
1
reply
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
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
1
vote
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
0
votes
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
0
votes
1
reply
999
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
6.8 years ago Dario Strbenac ★ 1.6k
0
votes
1
reply
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
1
vote
1
reply
1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 90
1
vote
1
reply
1.9k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
1
reply
1.4k
views
GC content
EDASeq
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
0
votes
0
replies
1.5k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.3 years ago kbobowik • 0
0
votes
0
replies
704
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
4.7 years ago abf ▴ 30
0
votes
0
replies
329
views
Are equal whisker lengths important in an RLE plot?
EDASeq EDA
7 months ago BioinfGuru ▴ 70
37 results • Page 1 of 1
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Comment: Package developing and interoperation with Bioconductor by shepherl 4.1k
Using an example with SummarizedExperiment would satisfy the requirement; however the package should take the object directly and not just…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Sofia • 0
1. I have tried to update the packages and R but to no avail. I keep getting either this error or : `Error in H5Fclose(file$H5Identifier) …
Comment: Validity of SingleR with very small bulk RNAseq reference by Rohit • 0
Hi @nhaus So, what did you end up doing in such a scenario? I am facing a similar challenge
Comment: CpGs with genomic positions greater than the chromosome size in EPICv2? by Joshua Llano • 0
Thank you for your reply James. I was worried that it was my mistake.
Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Votes
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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