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estimateCellCounts
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Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
4.1 years ago
grayapply2009
• 0
0
votes
0
replies
1.0k
views
estimateCellCounts issue with EPIC array data in minfi
minfi
estimatecellcounts
5.6 years ago
a.webster
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0
votes
1
reply
2.0k
views
getSex error even when sex is provided
minfi
estimatecellcounts
getSex
preprocessQuantile
updated 5.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.8 years ago by
fgc
• 0
1
vote
1
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1.6k
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Limma with paired samples and SVA
limma
sva
duplicatecorrelation
estimatecellcounts
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
wliao
• 0
0
votes
1
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1.7k
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How to convert GenomicRatioSet to RGChannelSet in minfi::compartments()
minfi
estimateCellCounts
methylation
updated 6.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 6.9 years ago by
stewart999
▴ 10
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Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
gabriel.hoffman
▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded
by
W. Evan Johnson
▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis
by
Alejandro Reyes
★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object
by
Alejandro Reyes
★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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