Showing : probe • reset
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log transform in RMA normalization
Normalization probe Normalization probe
updated 5 months ago by ▴ 20 • written 10.0 years ago by ▴ 440
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112
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
5 months ago Fatemeh • 0
0
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1
reply
1.0k
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filtering on variance
probe affy probe affy
updated 21 months ago by 47k • written 15.2 years ago by ▴ 90
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326
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Probe Design questions
probe affy
2.4 years ago henry1995910343 • 0
4
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10
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1.4k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 2.7 years ago by 3.7k • written 2.7 years ago by ▴ 10
0
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8
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2.0k
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Combining 2 datasets from 2 different RNAseq experiments
deseq2 normalization probe
updated 2.9 years ago by 39k • written 2.9 years ago by • 0
0
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0
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264
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Program to calculate genetic distances with long sequences
probe go
2.9 years ago antoniorevail • 0
0
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5
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648
views
Does anyone have experience using the massiR package?
massiR microarray R probe
3.4 years ago Steve Lowe ▴ 10
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297
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massiR Extracting and Plotting Y Chr Probe Data
probe microarray
3.4 years ago Steve Lowe ▴ 10
0
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1
reply
511
views
Determining survival correlation among probes
annotation probe microarray
3.5 years ago sbrackett007 • 0
0
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4
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574
views
Cannot down load the "org.Hs.eg.db" completely
software error probe
updated 3.6 years ago by 25k • written 3.6 years ago by • 0
2
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4
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776
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SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC probe normalization GEOdata cancer
3.8 years ago s.goncalvesclaro ▴ 10
0
votes
2
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1.2k
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
3.9 years ago brendan.miller • 0
1
vote
3
replies
441
views
I can't install the package "matchprobes"
software error probe
updated 3.9 years ago by 62k • written 3.9 years ago by • 0
0
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0
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422
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How to merging multiple GSEs with different GPLs?
microarray probe R
4.0 years ago maryam.sabet • 0
0
votes
1
reply
759
views
MCLUST: finding the best number of Gaussian components to fit my data
software error microarray probe annotation
updated 4.0 years ago by 39k • written 4.0 years ago by • 0
0
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0
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901
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe affy probe affy
updated 4.1 years ago by 0 • written 19.0 years ago by ▴ 940
0
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3
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3.3k
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Use probesets with highest baseline expression for differential gene
Annotation probe limma
11.0 years ago • updated 4.4 years ago Gordon Smyth 47k
1
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2
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580
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 4.4 years ago by 62k • written 4.4 years ago by • 0
0
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2
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1.5k
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[ComBat] ComBat outputting NAs with Large Batches - Switch to Log Likelihood
probe probe
updated 4.9 years ago by • 0 • written 10.2 years ago by ▴ 10
0
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0
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798
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Probe annotations for ABI Human Genome Survey V2 microarray using Oracle
annotation probe microarray abi human genome survey v2 Oracle
4.9 years ago judemtaylor • 0
1
vote
3
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1.6k
views
GO terms: Annotation for HumanMethylation450
Annotation GO probe Annotation GO probe
updated 4.9 years ago by • 0 • written 9.9 years ago by ▴ 970
0
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1
reply
633
views
index of probes in Illumina Infinium MethylationEPIC BeadChip
probe
5.0 years ago mcarmel • 0
4
votes
5
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1.7k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray affymetrix probeset probe
updated 5.3 years ago by ★ 5.9k • written 5.3 years ago by • 0
0
votes
1
reply
909
views
Multiple samples on the same graph
Pathview probe
updated 5.5 years ago by ★ 1.6k • written 5.6 years ago by • 0
0
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1
reply
619
views
probe set-gene relation
probe geneid probeset
updated 5.8 years ago by 62k • written 5.8 years ago by • 0
0
votes
8
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1.3k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 5.9 years ago by ▴ 40 • written 16.4 years ago by ▴ 20
1
vote
6
replies
1.2k
views
Remove a list of specific probes from an HTAFeatureSet
pd.clariom.d.human affy probe
updated 5.9 years ago by 62k • written 5.9 years ago by ▴ 40
1
vote
5
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815
views
Filter out ranges by number of probes
probe ranges
updated 5.9 years ago by ★ 5.9k • written 5.9 years ago by ▴ 30
0
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0
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869
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removing probes representing in a certain beads
minfi probe preprocessing
6.0 years ago niutster • 0
0
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4
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1.5k
views
minfi probe removal
minfi probe
updated 6.0 years ago by 62k • written 6.0 years ago by • 0
3
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4
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4.4k
views
LIMMA and Agilent single color
Annotation probe limma agilent
12.1 years ago • updated 6.0 years ago Gordon Smyth 47k
0
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1
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1.5k
views
LIMMA and Agilent single color
probe limma probe limma
updated 6.1 years ago by 47k • written 12.1 years ago by ▴ 60
1
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4
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1.6k
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How to install old GenomicRanges 1.14.4 package ?
bioconductor R cancer probe deseq2
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by • 0
0
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1
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1.2k
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 6.8 years ago by 25k • written 6.8 years ago by • 0
0
votes
1
reply
940
views
Importing and Extracting Annotation
annotation zebrafish probe
updated 6.8 years ago by 62k • written 6.8 years ago by • 0
2
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3
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1.4k
views
i need AGI code as my probset
affy cdf probe
7.2 years ago • updated 7.0 years ago Angel ▴ 40
0
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5
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1.3k
views
"oligo" package: probenames/probeinfo different from expr-set (read.cellfles): miRNA 4.0 (affy)
microarray probe annotation affy
7.0 years ago dietmar.pils • 0
0
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0
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889
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Help for affy
affy process probe
7.0 years ago weizhong_2007 • 0
0
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3
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9.8k
views
How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 7.5 years ago by ▴ 800 • written 7.6 years ago by ▴ 10
1
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4
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1.0k
views
mutually add a tab in the beggining of the header to make it a valid RMA format
software error probe affy RMA
7.6 years ago Angel ▴ 40
2
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2
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2.0k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe annotation illimina 450k methylation minfi methylation
7.6 years ago metamaden ▴ 10
0
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5
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4.9k
views
How to do Affy ST array analysis
Annotation Normalization hgu133a probe affy oligo Annotation Normalization hgu133a probe
updated 7.7 years ago by • 0 • written 8.8 years ago by ★ 12k
0
votes
1
reply
1.1k
views
simpleaffy segmentation fault
Survival probe genefilter affy affyio Survival probe genefilter affy affyio
updated 7.7 years ago by • 0 • written 16.1 years ago by ▴ 170
0
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2
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891
views
difficulty in mapping gene names to probes coordinates in a celfile
microarray probe
updated 7.9 years ago by 62k • written 7.9 years ago by • 0
0
votes
2
replies
1.2k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 7.9 years ago by • 0 • written 18.3 years ago by ▴ 600
0
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3
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2.1k
views
filtering out probes with no gene symbol from expressionSet
probe filter subset gene symbol affy
7.9 years ago alakatos ▴ 120
1
vote
1
reply
1.4k
views
Coercion of MethyLumiSet to MethyLumiR changes raw methylation values?
Normalization probe lumi Normalization probe lumi
updated 8.0 years ago by • 0 • written 8.9 years ago by ▴ 20
1
vote
2
replies
1.4k
views
array quality control, affy probes, contracts setting in limma, result interpretation and weights
limma affy probe qualitycontrol design and contrast matrix
updated 8.1 years ago by 47k • written 8.1 years ago by ▴ 120
6
votes
2
replies
1.4k
views
Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?
miRNA cdf probe limma miRNA cdf probe limma
updated 8.4 years ago by 47k • written 8.5 years ago by ★ 12k
50 results • Page 1 of 1
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Replies
Comment: mas5calls function doesn't work; mirna40cdf problem by Guido Hooiveld ★ 3.5k
Also: you could consider using `DABG` for present/absent calls. James elaborated on this in this thread: https://support.bioconductor.org/p…
Comment: mas5calls function doesn't work; mirna40cdf problem by James W. MacDonald 62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem by Berna • 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage by ayabalbaa1990 • 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object by shaimaa • 0
I used the combat-seq but the deseq complain as its not integer what should i do
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
Awards • All
Popular Question to Guido Hooiveld ★ 3.5k
Scholar to James W. MacDonald 62k
Commentator to Michael Love 39k
Popular Question to twtoal ▴ 10
Student to L ▴ 40
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