Showing : Preprocessing • reset
3
votes
9
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1.9k
views
About the best use of frma for several GEO Series
frma normalization preprocessing
updated 7.3 years ago by ▴ 830 • written 7.4 years ago by ▴ 20
0
votes
7
replies
1.4k
views
rMAT tutorial. Data file too large?
Preprocessing GUI rMAT Preprocessing GUI rMAT
14.0 years ago Patrick Schorderet ▴ 50
0
votes
6
replies
1.7k
views
RMA vs VSN
Preprocessing vsn Preprocessing vsn
19.9 years ago Roger Vallejo ▴ 120
1
vote
6
replies
2.2k
views
How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 6.1 years ago by ★ 3.9k • written 6.1 years ago by ▴ 260
0
votes
6
replies
1.6k
views
limma
Preprocessing limma Preprocessing limma
13.1 years ago Gordon Smyth 50k
4
votes
6
replies
558
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
0
votes
6
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3.7k
views
using rma() on XYS files using oligo package
Annotation Preprocessing Annotation Preprocessing
updated 10.2 years ago by ★ 4.3k • written 10.2 years ago by ▴ 30
0
votes
6
replies
1.2k
views
farms package fails on estrogen data
Preprocessing Preprocessing
updated 14.1 years ago by 25k • written 14.1 years ago by ▴ 840
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
5
votes
5
replies
2.7k
views
Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing rnaseq microarray
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 30
0
votes
5
replies
1.1k
views
xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
Annotation Preprocessing probe oligo xps Annotation Preprocessing probe oligo xps
updated 15.2 years ago by ★ 3.9k • written 15.2 years ago by ▴ 270
0
votes
5
replies
1.4k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 60
0
votes
5
replies
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 14.5 years ago by ★ 4.3k • written 14.5 years ago by ▴ 840
5
votes
4
replies
1.7k
views
meta analysis of microarrays of small sample sizes
preprocessing microarray genemeta
updated 7.5 years ago by ▴ 110 • written 7.5 years ago by ▴ 20
0
votes
4
replies
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
4
replies
1.6k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 8.4 years ago by ★ 6.5k • written 8.4 years ago by • 0
0
votes
4
replies
1.5k
views
Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 13.0 years ago by ▴ 310 • written 13.0 years ago by ★ 8.2k
0
votes
4
replies
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
4
replies
1.4k
views
HTqPCR problems
qPCR GO Preprocessing GLAD HTqPCR qPCR GO Preprocessing GLAD HTqPCR
updated 11.8 years ago by ▴ 340 • written 11.8 years ago by ★ 2.0k
0
votes
4
replies
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
1
vote
4
replies
2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
0
votes
3
replies
853
views
suggestion : new object for exprSet
Preprocessing gcrma Preprocessing gcrma
updated 19.1 years ago by ★ 7.4k • written 19.1 years ago by ★ 1.8k
0
votes
3
replies
1.1k
views
RMA XPS Problem on MoGene 1.0 ST
Preprocessing Cancer xps Preprocessing Cancer xps
updated 13.5 years ago by ★ 3.9k • written 13.5 years ago by ▴ 20
0
votes
3
replies
1.0k
views
ad hoc tools for affy tiling arrays?
Normalization Preprocessing gcrma Normalization Preprocessing gcrma
updated 18.2 years ago by ▴ 310 • written 18.2 years ago by ★ 6.5k
0
votes
3
replies
2.6k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 410
0
votes
3
replies
2.2k
views
Minfi preprocessing and rs probes
Preprocessing minfi Preprocessing minfi
updated 11.4 years ago by ★ 6.5k • written 11.4 years ago by ▴ 440
0
votes
3
replies
2.6k
views
Inherits(x,"data.frame") error in SamR
Microarray Normalization Preprocessing Bayesian Clustering TimeCourse Cancer affy vsn LPE
18.2 years ago McGee, Monnie ▴ 300
0
votes
3
replies
1.9k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival
updated 13.0 years ago by ▴ 310 • written 13.0 years ago by ★ 8.2k
0
votes
3
replies
1.2k
views
LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 18.6 years ago by 50k • written 18.6 years ago by ▴ 270
0
votes
3
replies
1.1k
views
selecting/filtering probesets from exprSet object prior to diff. exp. anal.
Preprocessing genefilter limma Preprocessing genefilter limma
updated 12.4 years ago by 65k • written 12.4 years ago by ▴ 40
0
votes
3
replies
1.2k
views
Webbioc error exprSet vs expressionSet
Preprocessing multtest webbioc Preprocessing multtest webbioc
16.1 years ago Balasubramanian Ganesan ▴ 70
0
votes
3
replies
1.7k
views
Searching for packages for normalizing Metabolomic data
Preprocessing Preprocessing
updated 6.7 years ago by ▴ 10 • written 13.4 years ago by ▴ 60
0
votes
3
replies
2.6k
views
fold-change when no expression to high expression
GO Preprocessing GO Preprocessing
updated 14.9 years ago by ★ 13k • written 14.9 years ago by ▴ 180
0
votes
2
replies
901
views
ANN: Bioconductor short course June 1-3 in Seattle
Preprocessing Visualization Cancer Preprocessing Visualization Cancer
19.1 years ago Seth Falcon ★ 7.4k
2
votes
2
replies
1.3k
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
votes
2
replies
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
2
replies
809
views
Does hist (affy) function work on probe-pair values or probe-set values?
Preprocessing probe graph Preprocessing probe graph
updated 14.5 years ago by ★ 2.0k • written 14.5 years ago by ▴ 840
0
votes
2
replies
839
views
xps: returns only 21 records
Preprocessing Preprocessing
updated 14.1 years ago by ★ 3.9k • written 14.1 years ago by ▴ 330
0
votes
2
replies
1.1k
views
Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 11.2 years ago by ▴ 290 • written 11.2 years ago by ▴ 570
0
votes
2
replies
1.1k
views
Nimblegen / Ringo / Preprocess error: inherits(myRG, "RGList") is not TRUE
Preprocessing Homo sapiens probe Ringo Preprocessing Homo sapiens probe Ringo
14.9 years ago JEAN-YVES SGRO ▴ 20
0
votes
2
replies
997
views
Question on importing large dataset (1.4GB) into R-Bioconductor
Microarray Normalization Preprocessing Microarray Normalization Preprocessing
updated 14.8 years ago by 21k • written 14.8 years ago by ▴ 40
0
votes
2
replies
1.2k
views
preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing gcrma Microarray Normalization Preprocessing gcrma
updated 14.7 years ago by ★ 2.3k • written 14.7 years ago by ▴ 840
0
votes
2
replies
1.8k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 20
3
votes
2
replies
2.9k
views
Nanostring ncounterdata - DESeq
RNASeq Normalization Preprocessing DESeq RNASeq Normalization Preprocessing DESeq
updated 12.8 years ago by ★ 3.7k • written 12.8 years ago by ▴ 20
0
votes
2
replies
930
views
bead-level data from Infinium methylation arrays
Annotation Preprocessing Annotation Preprocessing
updated 14.8 years ago by ★ 1.1k • written 14.8 years ago by ▴ 160
0
votes
2
replies
1.3k
views
Agilent single color array
Normalization Preprocessing vsn limma Normalization Preprocessing vsn limma
updated 15.8 years ago by 21k • written 15.8 years ago by ★ 6.5k
0
votes
2
replies
1.0k
views
Preprocessing affymetrix data
Preprocessing Preprocessing
updated 18.7 years ago by ▴ 20 • written 18.7 years ago by ▴ 150
0
votes
2
replies
1.4k
views
ReadAffy crashes on mac
Preprocessing affy convert affxparser affyio BUS Preprocessing affy convert affxparser
updated 15.7 years ago by ★ 1.2k • written 15.7 years ago by ▴ 40
0
votes
2
replies
1.7k
views
summarizing probe intensites before or after normalization- 1. how to do with RMA 2. Opinions?
Microarray Normalization Preprocessing Cancer probe affy convert affyio Microarray Cancer
17.6 years ago James W. MacDonald 65k
0
votes
2
replies
1.1k
views
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
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Votes
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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