Showing : Preprocessing • reset
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
0
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3
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2.6k
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Inherits(x,"data.frame") error in SamR
Microarray Normalization Preprocessing Bayesian Clustering TimeCourse Cancer affy vsn LPE
18.3 years ago McGee, Monnie ▴ 300
0
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6
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1.6k
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limma
Preprocessing limma Preprocessing limma
13.1 years ago Gordon Smyth 50k
0
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2
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1.1k
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preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing affy gcrma Microarray Normalization Preprocessing
updated 14.7 years ago by ★ 3.9k • written 14.7 years ago by ▴ 840
0
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3
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1.2k
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Webbioc error exprSet vs expressionSet
Preprocessing multtest webbioc Preprocessing multtest webbioc
16.1 years ago Balasubramanian Ganesan ▴ 70
0
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2
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1.0k
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Preprocessing affymetrix data
Preprocessing Preprocessing
updated 18.8 years ago by ▴ 20 • written 18.8 years ago by ▴ 150
0
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2
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1.2k
views
Nimblegen / Ringo / Preprocess error: inherits(myRG, "RGList") is not TRUE
Preprocessing Homo sapiens probe Ringo Preprocessing Homo sapiens probe Ringo
15.0 years ago JEAN-YVES SGRO ▴ 20
0
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2
replies
829
views
Does hist (affy) function work on probe-pair values or probe-set values?
Preprocessing probe graph Preprocessing probe graph
updated 14.6 years ago by ★ 2.0k • written 14.6 years ago by ▴ 840
0
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3
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2.7k
views
fold-change when no expression to high expression
GO Preprocessing GO Preprocessing
updated 15.0 years ago by ★ 13k • written 15.0 years ago by ▴ 180
2
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2
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1.4k
views
AgilentG4502A_07_2 and AgilentG4502A_07_1
limma read.maimages normalization preprocessing
updated 6.4 years ago by 50k • written 6.4 years ago by ▴ 10
0
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3
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1.7k
views
Searching for packages for normalizing Metabolomic data
Preprocessing Preprocessing
updated 6.7 years ago by ▴ 10 • written 13.5 years ago by ▴ 60
0
votes
6
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1.2k
views
farms package fails on estrogen data
Preprocessing Preprocessing
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 840
0
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2
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912
views
ANN: Bioconductor short course June 1-3 in Seattle
Preprocessing Visualization Cancer Preprocessing Visualization Cancer
19.1 years ago Seth Falcon ★ 7.4k
0
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7
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1.4k
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rMAT tutorial. Data file too large?
Preprocessing GUI rMAT Preprocessing GUI rMAT
14.1 years ago Patrick Schorderet ▴ 50
0
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5
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1.4k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.1 years ago by ★ 13k • written 14.1 years ago by ▴ 60
0
votes
4
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1.5k
views
Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 13.1 years ago by ▴ 310 • written 13.1 years ago by ★ 8.2k
0
votes
4
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2.9k
views
convert gene name to Affy ID
Preprocessing Preprocessing
updated 11.4 years ago by ▴ 10 • written 11.4 years ago by ★ 13k
0
votes
4
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1.6k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 8.4 years ago by ★ 6.5k • written 8.5 years ago by • 0
0
votes
3
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1.9k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival
updated 13.1 years ago by ▴ 310 • written 13.1 years ago by ★ 8.2k
0
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3
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1.0k
views
ad hoc tools for affy tiling arrays?
Normalization Preprocessing gcrma Normalization Preprocessing gcrma
updated 18.3 years ago by ▴ 310 • written 18.3 years ago by ★ 6.5k
0
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2
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1.0k
views
Question on importing large dataset (1.4GB) into R-Bioconductor
Microarray Normalization Preprocessing Microarray Normalization Preprocessing
updated 14.9 years ago by 21k • written 14.9 years ago by ▴ 40
0
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6
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1.8k
views
RMA vs VSN
Preprocessing vsn Preprocessing vsn
19.9 years ago Roger Vallejo ▴ 120
0
votes
2
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1.1k
views
Error in gammaFitEM for library(lumi) [Possible Bug]
Preprocessing Network Preprocessing Network
updated 12.3 years ago by ▴ 440 • written 12.3 years ago by ▴ 10
0
votes
3
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1.2k
views
LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 18.7 years ago by 50k • written 18.7 years ago by ▴ 270
0
votes
1
reply
704
views
Biostrings pdf, missing? 'Efficient genome searching with Biostrings and the BSgenome data package'
Preprocessing BSgenome Biostrings BSgenome Preprocessing BSgenome Biostrings BSgenome
updated 13.6 years ago by ★ 8.2k • written 13.6 years ago by ★ 1.1k
0
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3
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879
views
suggestion : new object for exprSet
Preprocessing gcrma Preprocessing gcrma
updated 19.2 years ago by ★ 7.4k • written 19.2 years ago by ★ 1.8k
0
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5
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1.4k
views
Imitating Affy's own steps
Microarray Normalization GO Preprocessing gcrma Microarray Normalization GO Preprocessing
updated 14.1 years ago by 65k • written 14.1 years ago by ▴ 120
0
votes
3
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1.1k
views
RMA XPS Problem on MoGene 1.0 ST
Preprocessing Cancer xps Preprocessing Cancer xps
updated 13.6 years ago by ★ 3.9k • written 13.6 years ago by ▴ 20
0
votes
4
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1.2k
views
affyPara: background correction & normalization only?
Preprocessing affy affyPara Preprocessing affy affyPara
updated 14.2 years ago by ▴ 380 • written 14.2 years ago by ▴ 30
0
votes
1
reply
763
views
error with getMeasureRepAgreement()
Preprocessing Preprocessing
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 80
0
votes
2
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1.3k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 14.2 years ago by ★ 1.2k • written 14.2 years ago by ★ 4.3k
0
votes
5
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2.1k
views
Analysing Human Gene ST 1.0 Arrays with oligo and oneChannelGUI yield different number of probesets
Preprocessing cdf oligo oneChannelGUI Preprocessing cdf oligo oneChannelGUI
updated 14.6 years ago by ★ 4.3k • written 14.6 years ago by ▴ 840
0
votes
1
reply
1.1k
views
Problem with rma function in xps package with Affymetrix Human Gene 1.0 ST Array
Preprocessing PROcess xps Preprocessing PROcess xps
updated 14.6 years ago by ★ 3.9k • written 14.6 years ago by ▴ 170
0
votes
1
reply
1.1k
views
Please Help with rMAT: NAs in Enrich Object
Normalization Preprocessing rtracklayer IRanges rMAT Normalization Preprocessing IRanges
updated 14.5 years ago by 25k • written 14.5 years ago by ▴ 410
0
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2
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855
views
xps: returns only 21 records
Preprocessing Preprocessing
updated 14.2 years ago by ★ 3.9k • written 14.2 years ago by ▴ 330
0
votes
2
replies
944
views
bead-level data from Infinium methylation arrays
Annotation Preprocessing Annotation Preprocessing
updated 14.9 years ago by ★ 1.1k • written 14.9 years ago by ▴ 160
0
votes
1
reply
885
views
network analyses on genes or probesets
Microarray Annotation Normalization Preprocessing Network Microarray Annotation Network
updated 15.2 years ago by ★ 7.2k • written 15.2 years ago by ▴ 380
0
votes
1
reply
2.0k
views
Entrez Gene ID to Probe Set Name
aCGH Sequencing miRNA Microarray Annotation Normalization GO Preprocessing Visualization
updated 15.6 years ago by ★ 7.2k • written 15.6 years ago by ▴ 300
0
votes
4
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1.2k
views
Multiple test question in micrarray- FDR
GO Preprocessing GO Preprocessing
updated 15.4 years ago by ▴ 220 • written 15.4 years ago by ★ 6.0k
0
votes
1
reply
1.1k
views
GCRMA
Microarray Preprocessing gcrma BRAIN Microarray Preprocessing gcrma BRAIN
updated 18.3 years ago by ★ 2.0k • written 18.3 years ago by ▴ 20
0
votes
1
reply
918
views
compare expression measures (and AffyComp)
Preprocessing affycomp Preprocessing affycomp
updated 18.4 years ago by 21k • written 18.4 years ago by ▴ 520
0
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1
reply
1.4k
views
Normalization of Agilent miRNA arrays using spike-ins
miRNA Normalization Preprocessing vsn limma miRNA Normalization Preprocessing vsn limma
updated 15.6 years ago by ★ 13k • written 15.6 years ago by ▴ 60
0
votes
5
replies
1.2k
views
xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
Annotation Preprocessing probe oligo xps Annotation Preprocessing probe oligo xps
updated 15.3 years ago by ★ 3.9k • written 15.3 years ago by ▴ 270
0
votes
2
replies
1.2k
views
preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing gcrma Microarray Normalization Preprocessing gcrma
updated 14.8 years ago by ★ 2.3k • written 14.8 years ago by ▴ 840
0
votes
1
reply
1.2k
views
number of Replicates - Fold change vs Limma or Siggenes/SAM
Preprocessing gcrma Preprocessing gcrma
updated 20.0 years ago by ▴ 30 • written 20.0 years ago by ▴ 90
0
votes
1
reply
929
views
kOverA(k, A=100, na.rm=TRUE)
GO Preprocessing Cancer genefilter limma GO Preprocessing Cancer genefilter limma
updated 15.9 years ago by ★ 5.5k • written 15.9 years ago by ▴ 30
0
votes
1
reply
1.0k
views
questions about Affy package from new user
Proteomics Normalization GO Preprocessing Clustering probe affy PROcess mscalib GO probe
updated 20.2 years ago by 65k • written 20.2 years ago by ▴ 210
0
votes
1
reply
809
views
Agilent single color array
Normalization Preprocessing vsn limma Normalization Preprocessing vsn limma
updated 15.9 years ago by ★ 6.5k • written 15.9 years ago by ▴ 400
0
votes
1
reply
2.2k
views
Recurrent error with Flashclust
Normalization Preprocessing probe Normalization Preprocessing probe
updated 13.3 years ago by ★ 3.0k • written 13.3 years ago by ▴ 340
0
votes
1
reply
988
views
kOverA(k, A=100, na.rm=TRUE)
GO Preprocessing genefilter limma GO Preprocessing genefilter limma
updated 15.9 years ago by ★ 5.5k • written 15.9 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Answer: How to run allelic imbalance in apeglm by Michael Love 42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22 by James W. MacDonald 65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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