Showing : Preprocessing • reset
4
votes
6
replies
560
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
1
vote
4
replies
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
replies
973
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
replies
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
votes
0
replies
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
votes
0
replies
1.1k
views
removing probes representing in a certain beads
minfi probe preprocessing
7.2 years ago niutster • 0
3
votes
9
replies
1.9k
views
About the best use of frma for several GEO Series
frma normalization preprocessing
updated 7.3 years ago by ▴ 830 • written 7.4 years ago by ▴ 20
5
votes
4
replies
1.7k
views
meta analysis of microarrays of small sample sizes
preprocessing microarray genemeta
updated 7.5 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
replies
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
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 8.8 years ago by 65k • written 8.8 years ago by • 0
0
votes
0
replies
1.1k
views
virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
9.6 years ago Guest User ★ 13k
0
votes
0
replies
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
replies
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
replies
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
replies
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
replies
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
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
869
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
replies
1.2k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
10.9 years ago Bade ▴ 310
0
votes
0
replies
2.8k
views
Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
10.9 years ago Gordon Smyth 50k
0
votes
0
replies
1.1k
views
virtualArray package - Error while combing data sets
Preprocessing virtualArray Preprocessing virtualArray
10.9 years ago Bade ▴ 310
0
votes
0
replies
966
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
votes
1
reply
1.3k
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ▴ 290
0
votes
0
replies
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
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 11.2 years ago by ▴ 290 • written 11.2 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
11.3 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
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
1.0k
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
replies
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
874
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
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Awards • All
Popular Question to James W. MacDonald 65k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Locations • All
Portugal, just now
France, 3 minutes ago
United Kingdom, 5 minutes ago
United States, 11 minutes ago
United States, 13 minutes ago
Traffic: 1045 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6