Showing : probe • reset
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
9 months ago jamiecatalano2 • 0
0
votes
11
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3.2k
views
globaltest question
Pathways probe affy Pathways probe affy
written 19.4 years ago by ▴ 30
2
votes
2
replies
8.3k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 3.5 years ago by ▴ 200 • written 13.1 years ago by ▴ 450
0
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0
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857
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
3.5 years ago Fatemeh • 0
0
votes
1
reply
2.0k
views
filtering on variance
probe affy probe affy
updated 4.8 years ago by 53k • written 18.2 years ago by ▴ 90
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0
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1.1k
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Probe Design questions
probe affy
5.4 years ago henry1995910343 • 0
4
votes
10
replies
5.0k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
0
votes
8
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6.5k
views
Combining 2 datasets from 2 different RNAseq experiments
deseq2 normalization probe
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
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0
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732
views
Program to calculate genetic distances with long sequences
probe go
6.0 years ago antoniorevail • 0
0
votes
5
replies
1.8k
views
Does anyone have experience using the massiR package?
massiR microarray R probe
6.4 years ago Steve Lowe ▴ 30
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0
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905
views
massiR Extracting and Plotting Y Chr Probe Data
probe microarray
6.5 years ago Steve Lowe ▴ 30
0
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1
reply
1.1k
views
Determining survival correlation among probes
annotation probe microarray
6.5 years ago sbrackett007 • 0
0
votes
4
replies
2.0k
views
Cannot down load the "org.Hs.eg.db" completely
software error probe
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
2
votes
4
replies
1.9k
views
SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC probe normalization GEOdata cancer
6.9 years ago s.goncalvesclaro ▴ 10
0
votes
2
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3.1k
views
liftover probe annotation from hg19 to hg38 for methylation array data using minfi (EPIC methylation array data)
annotation probe software error EPIC methylation array
6.9 years ago brendan.miller • 0
1
vote
3
replies
1.2k
views
I can't install the package "matchprobes"
software error probe
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
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0
replies
1.0k
views
How to merging multiple GSEs with different GPLs?
microarray probe R
7.0 years ago maryam.sabet • 0
0
votes
1
reply
1.6k
views
MCLUST: finding the best number of Gaussian components to fit my data
software error microarray probe annotation
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
0
replies
1.4k
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe affy probe affy
updated 7.1 years ago by 0 • written 22.0 years ago by ▴ 940
0
votes
3
replies
5.0k
views
Use probesets with highest baseline expression for differential gene
Annotation probe limma
14.0 years ago • updated 7.4 years ago Gordon Smyth 53k
1
vote
2
replies
1.6k
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
0
votes
2
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2.4k
views
[ComBat] ComBat outputting NAs with Large Batches - Switch to Log Likelihood
probe probe
updated 7.9 years ago by • 0 • written 13.2 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Probe annotations for ABI Human Genome Survey V2 microarray using Oracle
annotation probe microarray abi human genome survey v2 Oracle
7.9 years ago judemtaylor • 0
1
vote
3
replies
2.6k
views
GO terms: Annotation for HumanMethylation450
Annotation GO probe Annotation GO probe
updated 7.9 years ago by • 0 • written 12.9 years ago by ▴ 970
0
votes
1
reply
1.7k
views
index of probes in Illumina Infinium MethylationEPIC BeadChip
probe
8.1 years ago mcarmel • 0
4
votes
5
replies
3.2k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray affymetrix probeset probe
updated 8.4 years ago by ★ 6.6k • written 8.4 years ago by • 0
0
votes
1
reply
1.7k
views
Multiple samples on the same graph
Pathview probe
updated 8.6 years ago by ★ 1.6k • written 8.6 years ago by • 0
0
votes
1
reply
1.3k
views
probe set-gene relation
probe geneid probeset
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
0
votes
8
replies
2.9k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 8.9 years ago by ▴ 40 • written 19.4 years ago by ▴ 20
1
vote
6
replies
2.4k
views
Remove a list of specific probes from an HTAFeatureSet
pd.clariom.d.human affy probe
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 40
1
vote
5
replies
1.7k
views
Filter out ranges by number of probes
probe ranges
updated 9.0 years ago by ★ 6.6k • written 9.0 years ago by ▴ 30
0
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0
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1.4k
views
removing probes representing in a certain beads
minfi probe preprocessing
9.0 years ago niutster • 0
0
votes
4
replies
2.3k
views
minfi probe removal
minfi probe
updated 9.0 years ago by 68k • written 9.0 years ago by • 0
3
votes
4
replies
5.8k
views
LIMMA and Agilent single color
Annotation probe limma agilent
15.2 years ago • updated 9.1 years ago Gordon Smyth 53k
0
votes
1
reply
2.2k
views
LIMMA and Agilent single color
probe limma probe limma
updated 9.1 years ago by 53k • written 15.2 years ago by ▴ 60
1
vote
4
replies
2.8k
views
How to install old GenomicRanges 1.14.4 package ?
bioconductor R cancer probe deseq2
updated 9.7 years ago by ▴ 10 • written 9.8 years ago by • 0
0
votes
1
reply
1.7k
views
'could not find function "R (>= 2.1"' while trying https://bioconductor.org/packages/3.2/bioc, trying https://bioconductor.org/packages/3.1/bioc …
cancer probe microarray
updated 9.8 years ago by 25k • written 9.8 years ago by • 0
0
votes
1
reply
1.9k
views
Importing and Extracting Annotation
annotation zebrafish probe
updated 9.8 years ago by 68k • written 9.9 years ago by • 0
2
votes
3
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2.4k
views
i need AGI code as my probset
affy cdf probe
10.2 years ago • updated 10.0 years ago Angel ▴ 40
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votes
5
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2.2k
views
"oligo" package: probenames/probeinfo different from expr-set (read.cellfles): miRNA 4.0 (affy)
microarray probe annotation affy
10.0 years ago dietmar.pils • 0
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0
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1.5k
views
Help for affy
affy process probe
10.1 years ago weizhong_2007 • 0
0
votes
3
replies
13k
views
How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 10.6 years ago by ▴ 840 • written 10.6 years ago by ▴ 10
1
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4
replies
2.0k
views
mutually add a tab in the beggining of the header to make it a valid RMA format
software error probe affy RMA
10.6 years ago Angel ▴ 40
2
votes
2
replies
3.4k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe annotation illimina 450k methylation minfi methylation
10.6 years ago metamaden ▴ 10
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5
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6.2k
views
How to do Affy ST array analysis
Annotation Normalization hgu133a probe affy oligo Annotation Normalization hgu133a probe
updated 10.7 years ago by • 0 • written 11.8 years ago by ★ 13k
0
votes
1
reply
2.0k
views
simpleaffy segmentation fault
Survival probe genefilter affy affyio Survival probe genefilter affy affyio
updated 10.7 years ago by • 0 • written 19.1 years ago by ▴ 170
0
votes
2
replies
1.5k
views
difficulty in mapping gene names to probes coordinates in a celfile
microarray probe
updated 10.9 years ago by 68k • written 10.9 years ago by • 0
0
votes
2
replies
2.2k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 10.9 years ago by • 0 • written 21.4 years ago by ▴ 600
0
votes
3
replies
3.3k
views
filtering out probes with no gene symbol from expressionSet
probe filter subset gene symbol affy
11.0 years ago alakatos ▴ 130
1
vote
1
reply
2.3k
views
Coercion of MethyLumiSet to MethyLumiR changes raw methylation values?
Normalization probe lumi Normalization probe lumi
updated 11.0 years ago by • 0 • written 11.9 years ago by ▴ 20
1,388 results • Page 1 of 28
Recent ...
Replies
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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