Showing : preprocessing • reset
4
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6
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556
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
1
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4
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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
2
votes
2
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971
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
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
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
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 13.4 years ago by ▴ 60
0
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0
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1.2k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV minfi preprocessing dna methylation
7.1 years ago Thomas • 0
0
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0
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1.1k
views
removing probes representing in a certain beads
minfi probe preprocessing
7.2 years ago niutster • 0
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 7.3 years ago by ▴ 20
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
1
vote
1
reply
1.5k
views
Minfi RGChannelSet preprocessing error in assayDataElement
minfi preprocessing error
updated 7.6 years ago by ★ 6.5k • written 7.6 years ago by • 0
1
vote
0
replies
1.6k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
7.7 years ago t.kuilman ▴ 170
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 8.4 years ago by • 0
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
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1
reply
1.5k
views
The number of features of Expression Set for Affymetrix miRNA 4.0 data preprocsessed by oligo package
affy oligo microarray preprocessing microrna
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
0
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0
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1.1k
views
virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
9.6 years ago Guest User ★ 13k
0
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0
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1.1k
views
CRISPRseek: searchHits() optimization
Preprocessing BSgenome safe BSgenome CRISPRseek Preprocessing BSgenome safe BSgenome
9.7 years ago Julie Zhu ★ 4.3k
0
votes
0
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8.8k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
9.9 years ago Guest User ★ 13k
0
votes
0
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1.3k
views
GEOquery/virtualArray package error
Preprocessing hgu95av2 virtualArray Preprocessing hgu95av2 virtualArray
10.0 years ago Guest User ★ 13k
0
votes
1
reply
1.3k
views
Difference between GDS .Cel and series.matrix.txt
Normalization Preprocessing Normalization Preprocessing
updated 10.1 years ago by 21k • written 10.1 years ago by ▴ 150
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
2
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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
0
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1
reply
1.3k
views
Error in virtualArray Please help
Annotation Preprocessing Annotation Preprocessing
10.4 years ago Manvendra.Singh@mdc-berlin.de ▴ 20
0
votes
0
replies
867
views
New method for fully scalable preprocessing of large-scale gene expression atlases (RPA)
Microarray Preprocessing Microarray Preprocessing
10.5 years ago Leo Lahti ▴ 30
0
votes
0
replies
2.2k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
10.7 years ago Sarah Pohl ▴ 30
0
votes
1
reply
2.2k
views
Detecting differential usage of introns from RNA-seq data.
Preprocessing DEXSeq Preprocessing DEXSeq
updated 10.9 years ago by ★ 1.9k • written 10.9 years ago by ▴ 70
0
votes
0
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1.2k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
10.9 years ago Bade ▴ 310
0
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0
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2.8k
views
Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
10.9 years ago Gordon Smyth 50k
0
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0
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1.1k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
10.9 years ago Bade ▴ 310
0
votes
0
replies
964
views
Normalizing a dataset from GEO to suit a classifier trained on another dataset
Microarray Normalization Preprocessing probe affy preprocessCore frma Microarray probe
11.0 years ago Matthew McCall ▴ 830
0
votes
1
reply
1.8k
views
nsfilter error from expressionset obtained after using aroma for processing
Annotation Preprocessing hgu95av2 limma Annotation Preprocessing hgu95av2 limma
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 810
0
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1
reply
1.3k
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ▴ 290
0
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0
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1.2k
views
Detecting significant trends in variability
Microarray Preprocessing probe minfi Microarray Preprocessing probe minfi
11.2 years ago Gustavo Fernández Bayón ▴ 440
0
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0
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1.1k
views
Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
11.2 years ago Noah Dowell ▴ 410
0
votes
3
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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
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2
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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
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0
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1.2k
views
importing data problem with methyAnalysis package
Biophysics Annotation Preprocessing annotate lumi methyAnalysis Biophysics Annotation lumi
11.3 years ago Pan Du ▴ 440
0
votes
1
reply
1.1k
views
Bioconductor Digest, Vol 119, Issue 1
Preprocessing Homo sapiens affy oligo RPA Preprocessing Homo sapiens affy oligo RPA
updated 11.3 years ago by ▴ 20 • written 11.3 years ago by ▴ 30
0
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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
0
votes
1
reply
1.0k
views
PVAC and Affymetrix HuGene array
Preprocessing pvac Preprocessing pvac
updated 11.4 years ago by 65k • written 11.4 years ago by ▴ 10
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
0
replies
1.2k
views
segmentation fault in rma.background.correct()
GO Preprocessing AgiMicroRna GO Preprocessing AgiMicroRna
11.7 years ago Axel Klenk ★ 1.0k
0
votes
0
replies
1.1k
views
HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
11.7 years ago cfischer ▴ 10
0
votes
1
reply
1.4k
views
PDict in GenomicRanges
Preprocessing Cancer Preprocessing Cancer
11.7 years ago Hervé Pagès 16k
0
votes
4
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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
1
reply
964
views
oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values
Normalization Preprocessing probe oligo Normalization Preprocessing probe oligo
updated 11.8 years ago by ★ 4.3k • written 11.8 years ago by ★ 13k
0
votes
1
reply
872
views
Problem in filtering of single color microarrray data using LIMMA
Microarray Preprocessing limma PROcess Microarray Preprocessing limma PROcess
updated 11.9 years ago by ▴ 130 • written 11.9 years ago by ▴ 60
0
votes
0
replies
1.2k
views
Illumina beadarray analysis with lumi
Normalization Preprocessing probe PROcess beadarray lumi Normalization Preprocessing probe
12.0 years ago Ahmet ZEHIR ▴ 50
0
votes
1
reply
1.1k
views
for running arrayQualityMetrics
Preprocessing arrayQualityMetrics Preprocessing arrayQualityMetrics
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ★ 4.3k
0
votes
0
replies
1.8k
views
reading with lumi
Preprocessing PROcess lumi methylumi Preprocessing PROcess lumi methylumi
12.2 years ago Tim Triche ★ 4.2k
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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