Showing : preprocessing • reset
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affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 10 months ago by 68k • written 10 months ago by • 0
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5
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1.2k
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preprocessENmix colnames Error
ENmix Preprocessing
18 months ago • updated 17 months ago Eve • 0
4
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6
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 23 months ago by 53k • written 2.0 years ago by • 0
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4
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6.3k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.2 years ago by • 0
2
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2
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1.6k
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by • 0
1
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6
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How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 7.8 years ago by ★ 4.1k • written 7.8 years ago by ▴ 260
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2
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1.8k
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AgilentG4502A_07_2 and AgilentG4502A_07_1
limma read.maimages normalization preprocessing
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
0
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3
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2.2k
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Searching for packages for normalizing Metabolomic data
Preprocessing Preprocessing
updated 8.4 years ago by ▴ 10 • written 15.2 years ago by ▴ 60
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0
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DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV minfi preprocessing dna methylation
8.8 years ago Thomas • 0
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removing probes representing in a certain beads
minfi probe preprocessing
9.0 years ago niutster • 0
3
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9
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2.9k
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About the best use of frma for several GEO Series
frma normalization preprocessing
updated 9.1 years ago by ▴ 830 • written 9.1 years ago by ▴ 20
5
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4
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2.4k
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meta analysis of microarrays of small sample sizes
preprocessing microarray genemeta
updated 9.3 years ago by ▴ 110 • written 9.3 years ago by ▴ 20
1
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1
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2.1k
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Minfi RGChannelSet preprocessing error in assayDataElement
minfi preprocessing error
updated 9.4 years ago by ★ 6.5k • written 9.4 years ago by • 0
1
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Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
9.4 years ago t.kuilman ▴ 170
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2.1k
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IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 10.1 years ago by ★ 6.6k • written 10.2 years ago by • 0
5
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5
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Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing rnaseq microarray
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 30
0
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1
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2.0k
views
The number of features of Expression Set for Affymetrix miRNA 4.0 data preprocsessed by oligo package
affy oligo microarray preprocessing microrna
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
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virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
11.4 years ago Guest User ★ 13k
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CRISPRseek: searchHits() optimization
Preprocessing BSgenome safe BSgenome CRISPRseek Preprocessing BSgenome safe BSgenome
11.5 years ago Julie Zhu ★ 4.3k
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virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
11.6 years ago Guest User ★ 13k
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GEOquery/virtualArray package error
Preprocessing hgu95av2 virtualArray Preprocessing hgu95av2 virtualArray
11.7 years ago Guest User ★ 13k
0
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1.8k
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Difference between GDS .Cel and series.matrix.txt
Normalization Preprocessing Normalization Preprocessing
updated 11.8 years ago by 21k • written 11.8 years ago by ▴ 150
0
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6
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4.5k
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using rma() on XYS files using oligo package
Annotation Preprocessing Annotation Preprocessing
updated 11.9 years ago by ★ 4.3k • written 11.9 years ago by ▴ 30
0
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2
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2.3k
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[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 12.0 years ago by ▴ 570 • written 12.0 years ago by ▴ 20
0
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1
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1.6k
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Error in virtualArray Please help
Annotation Preprocessing Annotation Preprocessing
12.1 years ago Manvendra.Singh@mdc-berlin.de ▴ 20
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New method for fully scalable preprocessing of large-scale gene expression atlases (RPA)
Microarray Preprocessing Microarray Preprocessing
12.2 years ago Leo Lahti ▴ 40
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2.6k
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makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
12.4 years ago Sarah Pohl ▴ 30
0
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1
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2.6k
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Detecting differential usage of introns from RNA-seq data.
Preprocessing DEXSeq Preprocessing DEXSeq
updated 12.6 years ago by ★ 1.9k • written 12.6 years ago by ▴ 70
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virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
12.6 years ago Bade ▴ 310
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0
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3.2k
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Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
12.6 years ago Gordon Smyth 53k
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1.5k
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virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
12.7 years ago Bade ▴ 310
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0
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1.4k
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Normalizing a dataset from GEO to suit a classifier trained on another dataset
Microarray Normalization Preprocessing probe affy preprocessCore frma Microarray probe
12.8 years ago Matthew McCall ▴ 830
0
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1
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2.1k
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nsfilter error from expressionset obtained after using aroma for processing
Annotation Preprocessing hgu95av2 limma Annotation Preprocessing hgu95av2 limma
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 810
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1
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1.7k
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Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 12.9 years ago by ▴ 570 • written 12.9 years ago by ▴ 290
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Detecting significant trends in variability
Microarray Preprocessing probe minfi Microarray Preprocessing probe minfi
12.9 years ago Gustavo Fernández Bayón ▴ 440
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Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
12.9 years ago Noah Dowell ▴ 410
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3.3k
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Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 410
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2
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1.5k
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Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 12.9 years ago by ▴ 290 • written 12.9 years ago by ▴ 570
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0
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1.5k
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importing data problem with methyAnalysis package
Biophysics Annotation Preprocessing annotate lumi methyAnalysis Biophysics Annotation lumi
13.0 years ago Pan Du ▴ 440
0
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1
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1.5k
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Bioconductor Digest, Vol 119, Issue 1
Preprocessing Homo sapiens affy oligo RPA Preprocessing Homo sapiens affy oligo RPA
updated 13.1 years ago by ▴ 20 • written 13.1 years ago by ▴ 40
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4
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3.7k
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convert gene name to Affy ID
Preprocessing Preprocessing
updated 13.1 years ago by ▴ 10 • written 13.1 years ago by ★ 13k
0
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1
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1.4k
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PVAC and Affymetrix HuGene array
Preprocessing pvac Preprocessing pvac
updated 13.2 years ago by 68k • written 13.2 years ago by ▴ 10
0
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3
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2.9k
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Minfi preprocessing and rs probes
Preprocessing minfi Preprocessing minfi
updated 13.2 years ago by ★ 6.5k • written 13.2 years ago by ▴ 440
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0
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1.6k
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segmentation fault in rma.background.correct()
GO Preprocessing AgiMicroRna GO Preprocessing AgiMicroRna
13.4 years ago Axel Klenk ★ 1.1k
0
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0
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1.4k
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HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
13.4 years ago cfischer ▴ 10
0
votes
1
reply
1.8k
views
PDict in GenomicRanges
Preprocessing Cancer Preprocessing Cancer
13.5 years ago Hervé Pagès 16k
0
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4
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2.0k
views
HTqPCR problems
qPCR GO Preprocessing GLAD HTqPCR qPCR GO Preprocessing GLAD HTqPCR
updated 13.6 years ago by ▴ 340 • written 13.6 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values
Normalization Preprocessing probe oligo Normalization Preprocessing probe oligo
updated 13.6 years ago by ★ 4.3k • written 13.6 years ago by ★ 13k
0
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1
reply
1.2k
views
Problem in filtering of single color microarrray data using LIMMA
Microarray Preprocessing limma PROcess Microarray Preprocessing limma PROcess
updated 13.6 years ago by ▴ 130 • written 13.6 years ago by ▴ 60
0
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0
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1.6k
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Illumina beadarray analysis with lumi
Normalization Preprocessing probe PROcess beadarray lumi Normalization Preprocessing probe
13.8 years ago Ahmet ZEHIR ▴ 50
175 results • Page 1 of 4
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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