Showing : edaseq • reset
0
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443
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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
12 months ago BioinfGuru ▴ 70
2
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3
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1.1k
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
12 months ago BioinfGuru ▴ 70
1
vote
4
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1.0k
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
17 months ago samuel.channon • 0
2
votes
2
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857
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between lane normalization upper quantile
EDASeq edgeR
17 months ago elesofi • 0
0
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1
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1.5k
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GC content
EDASeq
updated 3.2 years ago by ★ 4.9k • written 3.2 years ago by • 0
2
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6
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1.9k
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
4.3 years ago Saulius ▴ 10
2
votes
2
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1.8k
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EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.5 years ago • updated 4.2 years ago gprezza • 0
1
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2
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1.5k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.8 years ago gprezza • 0
0
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0
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788
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5.1 years ago abf ▴ 30
1
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1
reply
2.1k
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EDASeq gene length normalization
edaseq r rna-seq
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
1
vote
6
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1.5k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
4
votes
7
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2.2k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.7 years ago by 52k • written 5.7 years ago by ▴ 60
1
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1
reply
1.2k
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Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 100
0
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3
replies
1.4k
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Possibly bug in newSeqExpressionSet function
software error EDASeq
6.4 years ago jens • 0
1
vote
2
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1.7k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.6 years ago by ▴ 980 • written 6.6 years ago by ▴ 270
2
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3
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2.6k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.8 years ago by 43k • written 6.8 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
6.8 years ago kbobowik • 0
1
vote
9
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3.5k
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EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 6.9 years ago by ▴ 980 • written 6.9 years ago by ▴ 10
1
vote
1
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1.4k
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Mean-Variance Plot for Normalised Counts
EDASeq meanVarPlot
updated 7.2 years ago by ▴ 980 • written 7.2 years ago by ★ 1.6k
0
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1
reply
1.1k
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq meanVarPlot
7.2 years ago Dario Strbenac ★ 1.6k
2
votes
7
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26k
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use EDAseq normalized data as input of DESeq2
deseq2 edaseq
7.3 years ago zoppoli pietro ▴ 10
0
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1
reply
2.1k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 130
2
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5
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3.1k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq normalization hg38 biomart org.db
updated 7.8 years ago by ▴ 980 • written 7.8 years ago by • 0
6
votes
11
replies
4.1k
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 7.8 years ago by ▴ 50 • written 7.8 years ago by ▴ 840
1
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1
reply
2.0k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.8 years ago by ▴ 980 • written 7.8 years ago by ▴ 10
1
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2
replies
1.9k
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Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 9.2 years ago by ▴ 980 • written 9.2 years ago by • 0
2
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2
replies
3.6k
views
How is the mean-variance plot calculated?
edaseq
updated 9.3 years ago by ★ 13k • written 9.3 years ago by • 0
9
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7
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3.8k
views
How to use normalized values by EDASeq in edgeR?
edgeR EDASeq
updated 10.0 years ago by 52k • written 10.0 years ago by • 0
0
votes
4
replies
2.2k
views
False positives due to GC content correction - DESeq2
EDASeq DESeq2 EDASeq DESeq2
updated 11.1 years ago by 43k • written 11.1 years ago by ★ 13k
2
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1
reply
2.2k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization EDASeq DESeq2 Normalization EDASeq DESeq2
updated 11.2 years ago by 43k • written 11.2 years ago by ★ 13k
0
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3
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3.1k
views
EDASeq within normalization
Normalization EDASeq Normalization EDASeq
updated 11.9 years ago by ▴ 980 • written 11.9 years ago by ▴ 30
0
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1
reply
1.5k
views
problem with aveLogCPM.default in edgeR
edgeR EDASeq edgeR EDASeq
updated 12.3 years ago by 52k • written 12.3 years ago by ▴ 40
0
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1
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2.3k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.4 years ago Kasper Daniel Hansen ★ 6.5k
0
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1
reply
2.9k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 12.5 years ago by 52k • written 12.5 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 12.5 years ago by ★ 6.5k • written 12.5 years ago by 52k
0
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2
replies
2.3k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.6 years ago love ▴ 150
0
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4
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1.9k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 13.6 years ago by ▴ 980 • written 13.6 years ago by ▴ 500
37 results • Page 1 of 1
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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