Showing : vsn • reset
5
votes
6
replies
6.3k
views
proper transformation for differential expression in normalized log expression data
tcga rnaseq deseq2 vsn edger
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
3
votes
2
replies
5.6k
views
problem installing "vsn" on debian... gcc: error: unrecognized command line option -fstack-protector-strong
install vsn gcc debian
9.2 years ago regcl • 0
7
votes
3
replies
4.3k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 17 months ago by 50k • written 5.1 years ago by ▴ 70
0
votes
8
replies
3.2k
views
Reading Agilent files using read.maimages
Survival DynDoc genefilter tkWidgets affy vsn marray convert ArrayExpress Survival affy
updated 16.7 years ago by ▴ 20 • written 16.7 years ago by ▴ 100
0
votes
11
replies
3.0k
views
Very low P-values in limma
miRNA Microarray Normalization GO vsn limma microRNA miRNA Microarray Normalization GO
updated 14.5 years ago by ★ 1.3k • written 14.5 years ago by 50k
0
votes
5
replies
2.9k
views
vsn: meanSdPlot + MAlist
Normalization vsn limma convert Normalization vsn limma convert
updated 14.4 years ago by 25k • written 14.4 years ago by ★ 3.9k
0
votes
3
replies
2.9k
views
error in vsn package
vsn failure to read documentation error
updated 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 40
0
votes
0
replies
2.6k
views
Re: vsn error L-BFGS-B needs finite values of fn
Cancer vsn arrayMagic Cancer vsn arrayMagic
19.9 years ago Wolfgang Huber ★ 13k
0
votes
2
replies
2.6k
views
installing problem - preprocessCore, affy on linux platform
Biobase genefilter affy vsn gcrma matchprobes preprocessCore Biobase genefilter affy vsn
updated 15.6 years ago by ★ 6.5k • written 15.6 years ago by ▴ 20
0
votes
3
replies
2.5k
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
3
replies
2.5k
views
Error: could not find function "normalize.AffyBatch.vsn"
vsn
updated 7.2 years ago by 65k • written 7.2 years ago by • 0
0
votes
6
replies
2.4k
views
how to use negative controls to obtain scale and offset parameters then to normalize the whole protein microarray data by vsn method
vsn protein microarray normalization scale and offset parameters
8.6 years ago guojiegina • 0
0
votes
3
replies
2.2k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
2
votes
4
replies
2.2k
views
limma and minimum fold change
Microarray vsn limma Microarray vsn limma
updated 13.4 years ago by 21k • written 13.4 years ago by ▴ 70
0
votes
5
replies
2.2k
views
Single-channel GenePix analysis with Limma (bg correction, normalization, weights)
Microarray Normalization vsn limma ASSIGN Microarray Normalization vsn limma ASSIGN
updated 10.4 years ago by 50k • written 10.4 years ago by ▴ 40
0
votes
1
reply
2.2k
views
Importing RMA processed data into limma for eBayes
Microarray Normalization affy vsn limma PROcess xps Microarray Normalization affy vsn
10.3 years ago Matthew Thornton ▴ 350
0
votes
1
reply
2.1k
views
Removing batch effects
vsn gcrma vsn gcrma
updated 18.7 years ago by ▴ 210 • written 18.7 years ago by ▴ 310
0
votes
8
replies
2.1k
views
vsn preprocess with oligo package
vsn oligo oligoClasses vsn oligo oligoClasses
updated 11.3 years ago by 65k • written 11.3 years ago by ▴ 110
0
votes
2
replies
2.0k
views
Agilent 4x44 single color expression arrays
Normalization probe vsn limma gcrma Normalization probe vsn limma gcrma
16.6 years ago Ido M. Tamir ▴ 320
0
votes
8
replies
2.0k
views
AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 17.4 years ago by ▴ 190 • written 17.4 years ago by ★ 2.9k
0
votes
0
replies
1.8k
views
LIMMA: choice of offset value for background correction method "normexp"
vsn limma vsn limma
18.1 years ago Gordon Smyth 50k
0
votes
6
replies
1.8k
views
Normalisation of Agilent microRNA arrays using inbuilt controls?
GO Cancer vsn AgiMicroRna GO Cancer vsn AgiMicroRna
updated 14.2 years ago by ★ 3.6k • written 14.2 years ago by ★ 1.9k
0
votes
4
replies
1.8k
views
gc-rma and vsn normalization for rat microarray data
Microarray Annotation Normalization vsn bgx puma Microarray Annotation Normalization vsn
updated 13.9 years ago by ★ 4.3k • written 13.9 years ago by ▴ 60
0
votes
2
replies
1.7k
views
technical replicates (again!): a summary
GO Cancer vsn GO Cancer vsn
updated 20.1 years ago by ★ 6.0k • written 20.1 years ago by ★ 1.1k
0
votes
6
replies
1.7k
views
RMA vs VSN
Preprocessing vsn Preprocessing vsn
19.8 years ago Roger Vallejo ▴ 120
0
votes
1
reply
1.7k
views
Question: How does limma derives its logFC value in two colored arrays?
Yeast affy vsn limma Yeast affy vsn limma
updated 13.6 years ago by ▴ 350 • written 13.6 years ago by 50k
0
votes
6
replies
1.7k
views
Heatmaps for Agilent Single Color 4x44k using limma and vsn.
Annotation Normalization vsn limma Annotation Normalization vsn limma
updated 11.1 years ago by 65k • written 11.1 years ago by ▴ 50
4
votes
4
replies
1.6k
views
change all the negative value into positive value
vsn
3.4 years ago • updated 3.3 years ago yueli7 ▴ 20
0
votes
0
replies
1.6k
views
Limma: Very high logFC values
Preprocessing probe vsn limma Preprocessing probe vsn limma
16.6 years ago Gordon Smyth 50k
0
votes
0
replies
1.6k
views
Removing control probes and treating technical replicates in Agilent one colour data
Microarray GO vsn limma Microarray GO vsn limma
16.0 years ago eldridb@stud.ntnu.no ▴ 10
0
votes
2
replies
1.6k
views
MA plots + dye swap
Normalization vsn limma Normalization vsn limma
updated 14.2 years ago by ▴ 340 • written 14.2 years ago by ★ 3.9k
0
votes
0
replies
1.6k
views
Bioconductor Digest, Vol 121, Issue 29
miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn
11.1 years ago Matthew Thornton ▴ 350
0
votes
2
replies
1.6k
views
Can't load annotations with lumi
Microarray OneChannel Annotation Normalization probe Biobase annotate genefilter affy vsn
updated 15.4 years ago by ★ 1.2k • written 15.4 years ago by ▴ 280
0
votes
5
replies
1.6k
views
getBioC v1.2.22 & [R] v1.6.2
annotate edd genefilter geneplotter rhdf5 multtest ROC tkWidgets reposTools affy vsn
updated 21.1 years ago by ★ 3.9k • written 21.1 years ago by ▴ 70
4
votes
4
replies
1.5k
views
Where can I use the VSN source code in C++?
vsn r language C++ source code
updated 7.2 years ago by ▴ 730 • written 7.2 years ago by • 0
0
votes
2
replies
1.5k
views
normalize.AffyBatch.vsn with reference vsn object
vsn vsn
updated 12.0 years ago by ★ 13k • written 12.0 years ago by ▴ 30
0
votes
3
replies
1.5k
views
ChIP-chip sequence bias not removed
Normalization vsn Starr Normalization vsn Starr
updated 13.7 years ago by ▴ 50 • written 13.7 years ago by ▴ 230
1
vote
5
replies
1.5k
views
normalization of a miRNA microarray
normalization vsn eximir microarray miRNA
updated 8.6 years ago by ★ 13k • written 8.6 years ago by ▴ 50
0
votes
3
replies
1.5k
views
how to normalize by columns
Normalization affy vsn Normalization affy vsn
updated 18.9 years ago by 50k • written 18.9 years ago by ▴ 40
0
votes
5
replies
1.5k
views
Detection of differential expression using limma
Microarray Normalization vsn limma Microarray Normalization vsn limma
updated 15.5 years ago by ▴ 10 • written 15.5 years ago by ▴ 60
0
votes
9
replies
1.5k
views
P calls (VSN and RMA)
affy vsn affy vsn
updated 20.3 years ago by ▴ 20 • written 20.3 years ago by ▴ 360
0
votes
2
replies
1.5k
views
vsn and oligo (or xps?) packages for GeneST expression arrays
vsn oligo xps vsn oligo xps
updated 14.3 years ago by ★ 3.9k • written 14.3 years ago by ▴ 270
0
votes
3
replies
1.5k
views
limma's implementation of VSN
Normalization vsn limma Normalization vsn limma
updated 14.6 years ago by ★ 13k • written 14.6 years ago by ★ 3.9k
0
votes
3
replies
1.5k
views
Most diff exp genes are up-regulated... can this be true?
Microarray Normalization vsn limma siggenes Microarray Normalization vsn limma siggenes
11.4 years ago Peter Davidsen ▴ 210
0
votes
7
replies
1.5k
views
Different Normalizations
vsn vsn
updated 20.2 years ago by ▴ 30 • written 20.2 years ago by ▴ 130
0
votes
4
replies
1.4k
views
Re: technical replicates (again!): a summary
Microarray GO Cancer vsn Microarray GO Cancer vsn
updated 20.1 years ago by ★ 1.1k • written 20.1 years ago by 50k
0
votes
2
replies
1.4k
views
vsn on log2 transformed data?
vsn vsn
updated 17.9 years ago by ★ 13k • written 17.9 years ago by ▴ 50
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
4
replies
1.3k
views
Normalization of 2 color Nimblegen array
vsn vsn
updated 18.1 years ago by ▴ 60 • written 18.1 years ago by ▴ 490
0
votes
4
replies
1.3k
views
Error in load VSN library
vsn vsn
updated 20.5 years ago by 65k • written 20.5 years ago by ▴ 770
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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