Showing : Preprocessing • reset
4
votes
6
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653
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
2
votes
2
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1.0k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.3 years ago by ★ 4.1k • written 3.3 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 6.2 years ago by ★ 4.0k • written 6.2 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
replies
1.7k
views
Searching for packages for normalizing Metabolomic data
Preprocessing Preprocessing
updated 6.7 years ago by ▴ 10 • written 13.5 years ago by ▴ 60
0
votes
0
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1.2k
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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
7.3 years ago niutster • 0
3
votes
9
replies
2.0k
views
About the best use of frma for several GEO Series
frma normalization preprocessing
updated 7.4 years ago by ▴ 830 • written 7.4 years ago by ▴ 20
5
votes
4
replies
1.7k
views
meta analysis of microarrays of small sample sizes
preprocessing microarray genemeta
updated 7.6 years ago by ▴ 110 • written 7.6 years ago by ▴ 20
1
vote
1
reply
1.6k
views
Minfi RGChannelSet preprocessing error in assayDataElement
minfi preprocessing error
updated 7.7 years ago by ★ 6.5k • written 7.7 years ago by • 0
1
vote
0
replies
1.6k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
7.8 years ago t.kuilman ▴ 170
0
votes
4
replies
1.6k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 8.4 years ago by ★ 6.5k • written 8.5 years ago by • 0
5
votes
5
replies
2.7k
views
Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing rnaseq microarray
updated 8.5 years ago by 50k • written 8.5 years ago by ▴ 30
0
votes
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 8.9 years ago by 65k • written 8.9 years ago by • 0
0
votes
0
replies
1.1k
views
virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
9.7 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
9.8 years ago Julie Zhu ★ 4.3k
0
votes
0
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8.9k
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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1.4k
views
GEOquery/virtualArray package error
Preprocessing hgu95av2 virtualArray Preprocessing hgu95av2 virtualArray
10.1 years ago Guest User ★ 13k
0
votes
1
reply
1.4k
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
replies
3.8k
views
using rma() on XYS files using oligo package
Annotation Preprocessing Annotation Preprocessing
updated 10.3 years ago by ★ 4.3k • written 10.3 years ago by ▴ 30
0
votes
2
replies
1.9k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 20
0
votes
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
873
views
New method for fully scalable preprocessing of large-scale gene expression atlases (RPA)
Microarray Preprocessing Microarray Preprocessing
10.5 years ago Leo Lahti ▴ 40
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 11.0 years ago by ▴ 70
0
votes
0
replies
1.2k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
11.0 years ago Bade ▴ 310
0
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0
replies
2.9k
views
Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
11.0 years ago Gordon Smyth 50k
0
votes
0
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1.2k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
11.0 years ago Bade ▴ 310
0
votes
0
replies
978
views
Normalizing a dataset from GEO to suit a classifier trained on another dataset
Microarray Normalization Preprocessing probe affy preprocessCore frma Microarray probe
11.1 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
votes
1
reply
1.3k
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 11.2 years ago by ▴ 570 • written 11.2 years ago by ▴ 290
0
votes
0
replies
1.3k
views
Detecting significant trends in variability
Microarray Preprocessing probe minfi Microarray Preprocessing probe minfi
11.2 years ago Gustavo Fernández Bayón ▴ 440
0
votes
0
replies
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
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
2
replies
1.1k
views
Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 11.3 years ago by ▴ 290 • written 11.3 years ago by ▴ 570
0
votes
0
replies
1.2k
views
importing data problem with methyAnalysis package
Biophysics Annotation Preprocessing annotate lumi methyAnalysis Biophysics Annotation lumi
11.4 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 11.4 years ago by ▴ 20 • written 11.4 years ago by ▴ 40
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
0
votes
1
reply
1.1k
views
PVAC and Affymetrix HuGene array
Preprocessing pvac Preprocessing pvac
updated 11.5 years ago by 65k • written 11.5 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Minfi preprocessing and rs probes
Preprocessing minfi Preprocessing minfi
updated 11.5 years ago by ★ 6.5k • written 11.5 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
11.8 years ago Hervé Pagès 16k
0
votes
4
replies
1.5k
views
HTqPCR problems
qPCR GO Preprocessing GLAD HTqPCR qPCR GO Preprocessing GLAD HTqPCR
updated 11.9 years ago by ▴ 340 • written 11.9 years ago by ★ 2.0k
0
votes
1
reply
978
views
oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values
Normalization Preprocessing probe oligo Normalization Preprocessing probe oligo
updated 11.9 years ago by ★ 4.3k • written 11.9 years ago by ★ 13k
0
votes
1
reply
897
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
12.1 years ago Ahmet ZEHIR ▴ 50
0
votes
1
reply
1.2k
views
for running arrayQualityMetrics
Preprocessing arrayQualityMetrics Preprocessing arrayQualityMetrics
updated 12.2 years ago by ★ 13k • written 12.2 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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Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup() by Anna • 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…
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Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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