Showing : Preprocessing • reset
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
0
votes
3
replies
2.6k
views
Inherits(x,"data.frame") error in SamR
Microarray Normalization Preprocessing Bayesian Clustering TimeCourse Cancer affy vsn LPE
18.2 years ago McGee, Monnie ▴ 300
0
votes
6
replies
1.6k
views
limma
Preprocessing limma Preprocessing limma
13.1 years ago Gordon Smyth 50k
0
votes
2
replies
1.1k
views
preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing affy gcrma Microarray Normalization Preprocessing
updated 14.7 years ago by ★ 3.9k • written 14.7 years ago by ▴ 840
0
votes
3
replies
1.2k
views
Webbioc error exprSet vs expressionSet
Preprocessing multtest webbioc Preprocessing multtest webbioc
16.1 years ago Balasubramanian Ganesan ▴ 70
0
votes
2
replies
1.0k
views
Preprocessing affymetrix data
Preprocessing Preprocessing
updated 18.7 years ago by ▴ 20 • written 18.7 years ago by ▴ 150
0
votes
2
replies
1.1k
views
Nimblegen / Ringo / Preprocess error: inherits(myRG, "RGList") is not TRUE
Preprocessing Homo sapiens probe Ringo Preprocessing Homo sapiens probe Ringo
14.9 years ago JEAN-YVES SGRO ▴ 20
0
votes
2
replies
812
views
Does hist (affy) function work on probe-pair values or probe-set values?
Preprocessing probe graph Preprocessing probe graph
updated 14.5 years ago by ★ 2.0k • written 14.5 years ago by ▴ 840
0
votes
3
replies
2.6k
views
fold-change when no expression to high expression
GO Preprocessing GO Preprocessing
updated 14.9 years ago by ★ 13k • written 14.9 years ago by ▴ 180
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
6
replies
1.2k
views
farms package fails on estrogen data
Preprocessing Preprocessing
updated 14.1 years ago by 25k • written 14.1 years ago by ▴ 840
0
votes
2
replies
903
views
ANN: Bioconductor short course June 1-3 in Seattle
Preprocessing Visualization Cancer Preprocessing Visualization Cancer
19.1 years ago Seth Falcon ★ 7.4k
0
votes
7
replies
1.4k
views
rMAT tutorial. Data file too large?
Preprocessing GUI rMAT Preprocessing GUI rMAT
14.0 years ago Patrick Schorderet ▴ 50
0
votes
5
replies
1.4k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 60
0
votes
4
replies
1.5k
views
Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 13.0 years ago by ▴ 310 • written 13.0 years ago by ★ 8.2k
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
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
0
votes
3
replies
1.9k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival
updated 13.0 years ago by ▴ 310 • written 13.0 years ago by ★ 8.2k
0
votes
3
replies
1.0k
views
ad hoc tools for affy tiling arrays?
Normalization Preprocessing gcrma Normalization Preprocessing gcrma
updated 18.2 years ago by ▴ 310 • written 18.2 years ago by ★ 6.5k
0
votes
2
replies
999
views
Question on importing large dataset (1.4GB) into R-Bioconductor
Microarray Normalization Preprocessing Microarray Normalization Preprocessing
updated 14.8 years ago by 21k • written 14.8 years ago by ▴ 40
0
votes
6
replies
1.7k
views
RMA vs VSN
Preprocessing vsn Preprocessing vsn
19.9 years ago Roger Vallejo ▴ 120
0
votes
2
replies
1.1k
views
Error in gammaFitEM for library(lumi) [Possible Bug]
Preprocessing Network Preprocessing Network
updated 12.2 years ago by ▴ 440 • written 12.2 years ago by ▴ 10
0
votes
3
replies
1.2k
views
LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 18.6 years ago by 50k • written 18.7 years ago by ▴ 270
0
votes
1
reply
697
views
Biostrings pdf, missing? 'Efficient genome searching with Biostrings and the BSgenome data package'
Preprocessing BSgenome Biostrings BSgenome Preprocessing BSgenome Biostrings BSgenome
updated 13.6 years ago by ★ 8.2k • written 13.6 years ago by ★ 1.1k
0
votes
3
replies
853
views
suggestion : new object for exprSet
Preprocessing gcrma Preprocessing gcrma
updated 19.1 years ago by ★ 7.4k • written 19.1 years ago by ★ 1.8k
0
votes
5
replies
1.4k
views
Imitating Affy's own steps
Microarray Normalization GO Preprocessing gcrma Microarray Normalization GO Preprocessing
updated 14.1 years ago by 65k • written 14.1 years ago by ▴ 120
0
votes
3
replies
1.1k
views
RMA XPS Problem on MoGene 1.0 ST
Preprocessing Cancer xps Preprocessing Cancer xps
updated 13.6 years ago by ★ 3.9k • written 13.6 years ago by ▴ 20
0
votes
4
replies
1.2k
views
affyPara: background correction & normalization only?
Preprocessing affy affyPara Preprocessing affy affyPara
updated 14.2 years ago by ▴ 380 • written 14.2 years ago by ▴ 30
0
votes
1
reply
757
views
error with getMeasureRepAgreement()
Preprocessing Preprocessing
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 80
0
votes
2
replies
1.3k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 14.2 years ago by ★ 1.2k • written 14.2 years ago by ★ 4.3k
0
votes
5
replies
2.1k
views
Analysing Human Gene ST 1.0 Arrays with oligo and oneChannelGUI yield different number of probesets
Preprocessing cdf oligo oneChannelGUI Preprocessing cdf oligo oneChannelGUI
updated 14.5 years ago by ★ 4.3k • written 14.5 years ago by ▴ 840
0
votes
1
reply
1.1k
views
Problem with rma function in xps package with Affymetrix Human Gene 1.0 ST Array
Preprocessing PROcess xps Preprocessing PROcess xps
updated 14.5 years ago by ★ 3.9k • written 14.5 years ago by ▴ 170
0
votes
1
reply
1.1k
views
Please Help with rMAT: NAs in Enrich Object
Normalization Preprocessing rtracklayer IRanges rMAT Normalization Preprocessing IRanges
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 410
0
votes
2
replies
842
views
xps: returns only 21 records
Preprocessing Preprocessing
updated 14.1 years ago by ★ 3.9k • written 14.1 years ago by ▴ 330
0
votes
2
replies
932
views
bead-level data from Infinium methylation arrays
Annotation Preprocessing Annotation Preprocessing
updated 14.8 years ago by ★ 1.1k • written 14.8 years ago by ▴ 160
0
votes
1
reply
874
views
network analyses on genes or probesets
Microarray Annotation Normalization Preprocessing Network Microarray Annotation Network
updated 15.1 years ago by ★ 7.2k • written 15.1 years ago by ▴ 380
0
votes
1
reply
2.0k
views
Entrez Gene ID to Probe Set Name
aCGH Sequencing miRNA Microarray Annotation Normalization GO Preprocessing Visualization
updated 15.5 years ago by ★ 7.2k • written 15.5 years ago by ▴ 300
0
votes
4
replies
1.2k
views
Multiple test question in micrarray- FDR
GO Preprocessing GO Preprocessing
updated 15.4 years ago by ▴ 220 • written 15.4 years ago by ★ 6.0k
0
votes
1
reply
1.1k
views
GCRMA
Microarray Preprocessing gcrma BRAIN Microarray Preprocessing gcrma BRAIN
updated 18.3 years ago by ★ 2.0k • written 18.3 years ago by ▴ 20
0
votes
1
reply
907
views
compare expression measures (and AffyComp)
Preprocessing affycomp Preprocessing affycomp
updated 18.3 years ago by 21k • written 18.3 years ago by ▴ 520
0
votes
1
reply
1.3k
views
Normalization of Agilent miRNA arrays using spike-ins
miRNA Normalization Preprocessing vsn limma miRNA Normalization Preprocessing vsn limma
updated 15.5 years ago by ★ 13k • written 15.5 years ago by ▴ 60
0
votes
5
replies
1.1k
views
xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
Annotation Preprocessing probe oligo xps Annotation Preprocessing probe oligo xps
updated 15.2 years ago by ★ 3.9k • written 15.2 years ago by ▴ 270
0
votes
2
replies
1.2k
views
preprocessing Affymetrix with threestep and expresso
Microarray Normalization Preprocessing gcrma Microarray Normalization Preprocessing gcrma
updated 14.7 years ago by ★ 2.3k • written 14.7 years ago by ▴ 840
0
votes
1
reply
1.2k
views
number of Replicates - Fold change vs Limma or Siggenes/SAM
Preprocessing gcrma Preprocessing gcrma
updated 19.9 years ago by ▴ 30 • written 19.9 years ago by ▴ 90
0
votes
1
reply
922
views
kOverA(k, A=100, na.rm=TRUE)
GO Preprocessing Cancer genefilter limma GO Preprocessing Cancer genefilter limma
updated 15.8 years ago by ★ 5.5k • written 15.8 years ago by ▴ 30
0
votes
1
reply
1.0k
views
questions about Affy package from new user
Proteomics Normalization GO Preprocessing Clustering probe affy PROcess mscalib GO probe
updated 20.1 years ago by 65k • written 20.1 years ago by ▴ 210
0
votes
1
reply
804
views
Agilent single color array
Normalization Preprocessing vsn limma Normalization Preprocessing vsn limma
updated 15.8 years ago by ★ 6.5k • written 15.8 years ago by ▴ 400
0
votes
1
reply
2.2k
views
Recurrent error with Flashclust
Normalization Preprocessing probe Normalization Preprocessing probe
updated 13.2 years ago by ★ 3.0k • written 13.2 years ago by ▴ 340
0
votes
1
reply
973
views
kOverA(k, A=100, na.rm=TRUE)
GO Preprocessing genefilter limma GO Preprocessing genefilter limma
updated 15.8 years ago by ★ 5.5k • written 15.8 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
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)
Awards • All
Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
United States, 4 minutes ago
United States, 21 minutes ago
Singapore, 47 minutes ago
France, 1 hour ago
Egypt, 1 hour ago
Traffic: 519 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