Showing : BiSeq • reset
0
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1
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869
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Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.1 years ago thomas.koefoed • 0
0
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0
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959
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.6 years ago i.s.castanho • 0
0
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1
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1.2k
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How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
4.6 years ago akhaira • 0
0
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1
reply
927
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testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
4.7 years ago akhaira • 0
2
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8
replies
1.3k
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Reason for NA in table after beta regression?
biseq beta regression
4.7 years ago akhaira • 0
0
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0
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628
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What values to include for predictedMethNull in BiSeq
Biseq
4.7 years ago akhaira • 0
2
votes
10
replies
1.8k
views
How do you use the readBismark command in BiSeq properly?
BiSeq DMR
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
1
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0
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788
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Understanding ColData in BiSeq
BiSeq Coldata
4.8 years ago akhaira • 0
0
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1
reply
868
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.8 years ago AishaD • 0
0
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1
reply
813
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.9 years ago i.s.castanho • 0
0
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0
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942
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq Wald test Beta regression
6.1 years ago mira • 0
0
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1
reply
1.2k
views
Biseq installation error
biseq package installation r
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
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0
replies
1.1k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
6.6 years ago spr ▴ 10
0
votes
1
reply
1.3k
views
Problem in working with BiSeq - BSraw
dna methylation biseq
updated 7.2 years ago by 52k • written 7.2 years ago by • 0
0
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1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
7.9 years ago l.eijssen • 0
0
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3
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1.5k
views
BiSeq. Model beta regression on resampled data.
biseq methylation dmr analysis
updated 8.2 years ago by ▴ 130 • written 8.2 years ago by • 0
0
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6
replies
2.2k
views
BiSeq trimClusters error
biseq error trimClusters
updated 9.1 years ago by ▴ 130 • written 9.1 years ago by • 0
1
vote
0
replies
1.9k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
9.2 years ago enricoferrero ▴ 680
4
votes
4
replies
2.2k
views
Unable to read data using readBismark in BiSeq
BiSeq readBismark
updated 9.3 years ago by 68k • written 9.3 years ago by ▴ 460
1
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2
replies
2.9k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 9.4 years ago by ★ 6.5k • written 9.4 years ago by ▴ 680
2
votes
15
replies
3.7k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
9.9 years ago • updated 9.8 years ago mnaymik ▴ 10
0
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5
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2.4k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.9 years ago • updated 9.8 years ago maria.maqueda • 0
0
votes
3
replies
2.0k
views
BiSeq - readBismark error
BiSeq BiSeq
updated 11.1 years ago by ▴ 130 • written 11.1 years ago by ▴ 330
23 results • Page 1 of 1
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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
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