Showing : preprocessing • reset
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preprocessENmix colnames Error
ENmix Preprocessing
4 months ago Eve • 0
4
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6
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1.1k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 months ago by 52k • written 11 months ago by • 0
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4
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4.2k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.1 years ago by • 0
2
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2
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1.3k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.8 years ago by ★ 4.6k • written 3.9 years ago by • 0
1
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6
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2.5k
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How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 6.8 years ago by ★ 4.1k • written 6.8 years ago by ▴ 260
2
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2
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1.5k
views
AgilentG4502A_07_2 and AgilentG4502A_07_1
limma read.maimages normalization preprocessing
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 10
0
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3
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1.9k
views
Searching for packages for normalizing Metabolomic data
Preprocessing Preprocessing
updated 7.3 years ago by ▴ 10 • written 14.1 years ago by ▴ 60
0
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0
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1.4k
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DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV minfi preprocessing dna methylation
7.7 years ago Thomas • 0
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1.2k
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removing probes representing in a certain beads
minfi probe preprocessing
7.9 years ago niutster • 0
3
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9
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2.2k
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About the best use of frma for several GEO Series
frma normalization preprocessing
updated 8.0 years ago by ▴ 830 • written 8.0 years ago by ▴ 20
5
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4
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1.9k
views
meta analysis of microarrays of small sample sizes
preprocessing microarray genemeta
updated 8.2 years ago by ▴ 110 • written 8.2 years ago by ▴ 20
1
vote
1
reply
1.7k
views
Minfi RGChannelSet preprocessing error in assayDataElement
minfi preprocessing error
updated 8.3 years ago by ★ 6.5k • written 8.3 years ago by • 0
1
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0
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1.8k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
8.3 years ago t.kuilman ▴ 170
0
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4
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1.8k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 9.0 years ago by ★ 6.6k • written 9.1 years ago by • 0
5
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5
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2.9k
views
Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing rnaseq microarray
updated 9.1 years ago by 52k • written 9.1 years ago by ▴ 30
0
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1
reply
1.7k
views
The number of features of Expression Set for Affymetrix miRNA 4.0 data preprocsessed by oligo package
affy oligo microarray preprocessing microrna
updated 9.5 years ago by 67k • written 9.5 years ago by • 0
0
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0
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1.3k
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virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
10.3 years ago Guest User ★ 13k
0
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1.2k
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CRISPRseek: searchHits() optimization
Preprocessing BSgenome safe BSgenome CRISPRseek Preprocessing BSgenome safe BSgenome
10.4 years ago Julie Zhu ★ 4.3k
0
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9.3k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
10.5 years ago Guest User ★ 13k
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GEOquery/virtualArray package error
Preprocessing hgu95av2 virtualArray Preprocessing hgu95av2 virtualArray
10.7 years ago Guest User ★ 13k
0
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1
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1.6k
views
Difference between GDS .Cel and series.matrix.txt
Normalization Preprocessing Normalization Preprocessing
updated 10.7 years ago by 21k • written 10.7 years ago by ▴ 150
0
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6
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4.0k
views
using rma() on XYS files using oligo package
Annotation Preprocessing Annotation Preprocessing
updated 10.8 years ago by ★ 4.3k • written 10.8 years ago by ▴ 30
0
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2
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2.0k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ▴ 20
0
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1
reply
1.4k
views
Error in virtualArray Please help
Annotation Preprocessing Annotation Preprocessing
11.0 years ago Manvendra.Singh@mdc-berlin.de ▴ 20
0
votes
0
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990
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New method for fully scalable preprocessing of large-scale gene expression atlases (RPA)
Microarray Preprocessing Microarray Preprocessing
11.1 years ago Leo Lahti ▴ 40
0
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0
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2.4k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
11.3 years ago Sarah Pohl ▴ 30
0
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1
reply
2.3k
views
Detecting differential usage of introns from RNA-seq data.
Preprocessing DEXSeq Preprocessing DEXSeq
updated 11.5 years ago by ★ 1.9k • written 11.6 years ago by ▴ 70
0
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0
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1.3k
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virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
11.6 years ago Bade ▴ 310
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0
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3.0k
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Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
11.6 years ago Gordon Smyth 52k
0
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0
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1.3k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
11.6 years ago Bade ▴ 310
0
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0
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1.1k
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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
11.7 years ago Matthew McCall ▴ 830
0
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1
reply
1.9k
views
nsfilter error from expressionset obtained after using aroma for processing
Annotation Preprocessing hgu95av2 limma Annotation Preprocessing hgu95av2 limma
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ▴ 810
0
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1
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1.4k
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 11.8 years ago by ▴ 570 • written 11.8 years ago by ▴ 290
0
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0
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1.4k
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Detecting significant trends in variability
Microarray Preprocessing probe minfi Microarray Preprocessing probe minfi
11.8 years ago Gustavo Fernández Bayón ▴ 440
0
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1.2k
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Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
11.8 years ago Noah Dowell ▴ 410
0
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3
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2.9k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 410
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2
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1.3k
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Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 11.8 years ago by ▴ 290 • written 11.8 years ago by ▴ 570
0
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0
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1.3k
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importing data problem with methyAnalysis package
Biophysics Annotation Preprocessing annotate lumi methyAnalysis Biophysics Annotation lumi
12.0 years ago Pan Du ▴ 440
0
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1
reply
1.3k
views
Bioconductor Digest, Vol 119, Issue 1
Preprocessing Homo sapiens affy oligo RPA Preprocessing Homo sapiens affy oligo RPA
updated 12.0 years ago by ▴ 20 • written 12.0 years ago by ▴ 40
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4
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3.2k
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convert gene name to Affy ID
Preprocessing Preprocessing
updated 12.0 years ago by ▴ 10 • written 12.0 years ago by ★ 13k
0
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1
reply
1.2k
views
PVAC and Affymetrix HuGene array
Preprocessing pvac Preprocessing pvac
updated 12.1 years ago by 67k • written 12.1 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Minfi preprocessing and rs probes
Preprocessing minfi Preprocessing minfi
updated 12.1 years ago by ★ 6.5k • written 12.1 years ago by ▴ 440
0
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0
replies
1.4k
views
segmentation fault in rma.background.correct()
GO Preprocessing AgiMicroRna GO Preprocessing AgiMicroRna
12.3 years ago Axel Klenk ★ 1.0k
0
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0
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1.2k
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HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
12.3 years ago cfischer ▴ 10
0
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1
reply
1.5k
views
PDict in GenomicRanges
Preprocessing Cancer Preprocessing Cancer
12.4 years ago Hervé Pagès 16k
0
votes
4
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1.7k
views
HTqPCR problems
qPCR GO Preprocessing GLAD HTqPCR qPCR GO Preprocessing GLAD HTqPCR
updated 12.5 years ago by ▴ 340 • written 12.5 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values
Normalization Preprocessing probe oligo Normalization Preprocessing probe oligo
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ★ 13k
0
votes
1
reply
1.0k
views
Problem in filtering of single color microarrray data using LIMMA
Microarray Preprocessing limma PROcess Microarray Preprocessing limma PROcess
updated 12.5 years ago by ▴ 130 • written 12.5 years ago by ▴ 60
0
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0
replies
1.4k
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Illumina beadarray analysis with lumi
Normalization Preprocessing probe PROcess beadarray lumi Normalization Preprocessing probe
12.7 years ago Ahmet ZEHIR ▴ 50
0
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1
reply
1.3k
views
for running arrayQualityMetrics
Preprocessing arrayQualityMetrics Preprocessing arrayQualityMetrics
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ★ 4.3k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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