Showing : Preprocessing • reset
0
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for running arrayQualityMetrics
Preprocessing arrayQualityMetrics Preprocessing arrayQualityMetrics
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ★ 4.3k
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reading with lumi
Preprocessing PROcess lumi methylumi Preprocessing PROcess lumi methylumi
13.8 years ago Tim Triche ★ 4.2k
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2
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Error in gammaFitEM for library(lumi) [Possible Bug]
Preprocessing Network Preprocessing Network
updated 13.8 years ago by ▴ 440 • written 13.9 years ago by ▴ 10
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1
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1.5k
views
HTqPCR useful for ChIP data ?
Preprocessing Clustering HTqPCR Preprocessing Clustering HTqPCR
updated 3.1 years ago by • 0 • written 13.9 years ago by ▴ 10
0
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0
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971
views
preprocessing pipeline of aglient Custom GE 8x15k single color array
Preprocessing Preprocessing
14.0 years ago Justin ▴ 10
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3
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1.4k
views
selecting/filtering probesets from exprSet object prior to diff. exp. anal.
Preprocessing genefilter limma Preprocessing genefilter limma
updated 14.0 years ago by 68k • written 14.1 years ago by ▴ 40
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1.8k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
14.2 years ago Lavorgna Giovanni ▴ 80
3
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2
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3.4k
views
Nanostring ncounterdata - DESeq
RNASeq Normalization Preprocessing DESeq RNASeq Normalization Preprocessing DESeq
updated 14.4 years ago by ★ 3.8k • written 14.4 years ago by ▴ 20
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0
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695
views
How to mine interest data from NimbleGen oligo array
Preprocessing Preprocessing
14.4 years ago 陈娟 ▴ 70
0
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792
views
Problem about extracting interest data from NimbleGen oligo array
Annotation Preprocessing oligo Annotation Preprocessing oligo
14.4 years ago Benilton Carvalho ★ 4.3k
0
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1
reply
852
views
Paired tests using limma and beadarray
Annotation Preprocessing limma beadarray Annotation Preprocessing limma beadarray
14.6 years ago Gordon Smyth 53k
0
votes
3
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2.3k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival
updated 14.7 years ago by ▴ 310 • written 14.7 years ago by ★ 8.2k
0
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4
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1.9k
views
Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 14.7 years ago by ▴ 310 • written 14.7 years ago by ★ 8.2k
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6
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2.1k
views
limma
Preprocessing limma Preprocessing limma
14.7 years ago Gordon Smyth 53k
0
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1
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1.0k
views
transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma
Microarray Preprocessing limma beadarray Microarray Preprocessing limma beadarray
updated 14.7 years ago by ★ 3.6k • written 14.7 years ago by ★ 1.1k
0
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1
reply
1.2k
views
R: Recurrent error with Flashclust
Normalization Preprocessing probe Normalization Preprocessing probe
14.9 years ago • updated 14.8 years ago Manca Marco PATH ▴ 340
0
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1
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973
views
How can I obtain the expression set from an antibody microarray
Microarray Preprocessing Microarray Preprocessing
updated 14.9 years ago by ★ 13k • written 14.9 years ago by ▴ 60
0
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1
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2.6k
views
Recurrent error with Flashclust
Normalization Preprocessing probe Normalization Preprocessing probe
updated 14.9 years ago by ★ 3.0k • written 14.9 years ago by ▴ 340
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3
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1.4k
views
RMA XPS Problem on MoGene 1.0 ST
Preprocessing Cancer xps Preprocessing Cancer xps
updated 15.2 years ago by ★ 3.9k • written 15.2 years ago by ▴ 20
0
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1
reply
910
views
Biostrings pdf, missing? 'Efficient genome searching with Biostrings and the BSgenome data package'
Preprocessing BSgenome Biostrings BSgenome Preprocessing BSgenome Biostrings BSgenome
updated 15.2 years ago by ★ 8.2k • written 15.2 years ago by ★ 1.1k
0
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1
reply
970
views
error with getMeasureRepAgreement()
Preprocessing Preprocessing
updated 15.3 years ago by ★ 13k • written 15.3 years ago by ▴ 80
0
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0
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848
views
xps - creating ROOT scheme fi les
Annotation Preprocessing cdf PROcess oligo xps Annotation Preprocessing cdf PROcess xps
15.5 years ago Benilton Carvalho ★ 4.3k
0
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0
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916
views
Affymetrix GeneChip Human Gene 1.0 ST Batch Effect and Saturation
Preprocessing Preprocessing
15.6 years ago Dennis Ting ▴ 10
0
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0
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1.0k
views
pint (& segmentation)
aCGH Preprocessing Cancer aCGH pint aCGH Preprocessing Cancer aCGH pint
15.6 years ago Leo Lahti ▴ 10
0
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7
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2.0k
views
rMAT tutorial. Data file too large?
Preprocessing GUI rMAT Preprocessing GUI rMAT
15.6 years ago Patrick Schorderet ▴ 50
0
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5
replies
1.8k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 15.6 years ago by ★ 13k • written 15.6 years ago by ▴ 60
0
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0
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1.3k
views
hugene10stv1cdf
Preprocessing cdf Preprocessing cdf
15.6 years ago Anthony Bosco ▴ 500
0
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5
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1.8k
views
Imitating Affy's own steps
Microarray Normalization GO Preprocessing gcrma Microarray Normalization GO Preprocessing
updated 15.7 years ago by 68k • written 15.7 years ago by ▴ 120
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2
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1.1k
views
xps: returns only 21 records
Preprocessing Preprocessing
updated 15.7 years ago by ★ 3.9k • written 15.7 years ago by ▴ 330
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0
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869
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CN analysis on a small Affymetrix GWS6 data set (Was: Re: QC Affy 6.0 SNP arrays with crlmm or Oligo?)
Preprocessing Preprocessing
15.7 years ago Henrik Bengtsson ★ 2.4k
0
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6
replies
1.7k
views
farms package fails on estrogen data
Preprocessing Preprocessing
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 840
0
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4
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1.6k
views
affyPara: background correction & normalization only?
Preprocessing affy affyPara Preprocessing affy affyPara
updated 15.8 years ago by ▴ 380 • written 15.8 years ago by ▴ 30
0
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2
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1.6k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 15.8 years ago by ★ 1.2k • written 15.8 years ago by ★ 4.3k
0
votes
0
replies
914
views
BioC Course 27-29 Jan 10: Introduction to R and Bioconductor
Microarray Preprocessing Microarray Preprocessing
15.9 years ago Patrick Aboyoun ★ 1.6k
0
votes
0
replies
992
views
BioC Course 27-29 Jan 10: Introduction to R and Bioconductor
Sequencing Microarray Preprocessing Sequencing Microarray Preprocessing
16.0 years ago Patrick Aboyoun ★ 1.6k
0
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1
reply
1.4k
views
Please Help with rMAT: NAs in Enrich Object
Normalization Preprocessing rtracklayer IRanges rMAT Normalization Preprocessing IRanges
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 410
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0
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1.7k
views
samr Error in quantile.default
Preprocessing Preprocessing
16.0 years ago Steve Chatfield ▴ 10
0
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0
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1.0k
views
Training course at EBI, Cambridge, UK, Feb 1-5
Sequencing Microarray Annotation Normalization Preprocessing probe Sequencing Microarray
16.1 years ago Wolfgang Huber ★ 13k
0
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0
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1.3k
views
Analysing Human Gene ST 1.0 Arrays with oligo and, oneChannelGUI yield different number of probesets
Preprocessing oneChannelGUI Preprocessing oneChannelGUI
16.1 years ago rcaloger ▴ 500
0
votes
5
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2.7k
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 16.1 years ago by ★ 4.3k • written 16.1 years ago by ▴ 840
0
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1
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1.3k
views
Problem with rma function in xps package with Affymetrix Human Gene 1.0 ST Array
Preprocessing PROcess xps Preprocessing PROcess xps
updated 16.1 years ago by ★ 3.9k • written 16.1 years ago by ▴ 170
0
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2
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1.1k
views
Does hist (affy) function work on probe-pair values or probe-set values?
Preprocessing probe graph Preprocessing probe graph
updated 16.2 years ago by ★ 2.0k • written 16.2 years ago by ▴ 840
0
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2
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1.4k
views
preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing affy gcrma Microarray Normalization Preprocessing
updated 16.3 years ago by ★ 3.9k • written 16.3 years ago by ▴ 840
0
votes
2
replies
1.5k
views
preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing gcrma Microarray Normalization Preprocessing gcrma
updated 16.3 years ago by ★ 2.3k • written 16.3 years ago by ▴ 840
0
votes
0
replies
1.6k
views
LIMMA: Why does eBayes expression differ from observed?
Normalization Preprocessing probe vsn limma Normalization Preprocessing probe vsn limma
16.4 years ago Axel Klenk ★ 1.1k
0
votes
2
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1.3k
views
Question on importing large dataset (1.4GB) into R-Bioconductor
Microarray Normalization Preprocessing Microarray Normalization Preprocessing
updated 16.4 years ago by 21k • written 16.4 years ago by ▴ 40
0
votes
2
replies
1.3k
views
bead-level data from Infinium methylation arrays
Annotation Preprocessing Annotation Preprocessing
updated 16.4 years ago by ★ 1.1k • written 16.4 years ago by ▴ 160
0
votes
3
replies
3.4k
views
fold-change when no expression to high expression
GO Preprocessing GO Preprocessing
updated 16.5 years ago by ★ 13k • written 16.5 years ago by ▴ 180
0
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2
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1.6k
views
Nimblegen / Ringo / Preprocess error: inherits(myRG, "RGList") is not TRUE
Preprocessing Homo sapiens probe Ringo Preprocessing Homo sapiens probe Ringo
16.6 years ago JEAN-YVES SGRO ▴ 20
0
votes
0
replies
861
views
Introductory BioC Course 27-29 April 09: Analyzing Microarray Experiments
Microarray Annotation Preprocessing Microarray Annotation Preprocessing
16.7 years ago Patrick Aboyoun ★ 1.6k
175 results • Page 2 of 4
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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