Showing : vsn • reset
1
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
15 months ago Arend ▴ 10
7
votes
3
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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 5.2 years ago by ▴ 70
0
votes
3
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2.3k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
votes
5
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1.1k
views
In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 2.7 years ago by 50k • written 2.7 years ago by • 0
2
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3
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1.1k
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one stratum from vsn2
vsn vsn2 onestratum
updated 3.3 years ago by ★ 13k • written 3.3 years ago by • 0
4
votes
4
replies
1.6k
views
change all the negative value into positive value
vsn
3.4 years ago yueli7 ▴ 20
4
votes
4
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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
1
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2
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1.2k
views
Bug in vsn2 in package vsn?
vsn vsn2
updated 7.2 years ago by ★ 13k • written 7.2 years ago by ★ 3.0k
0
votes
3
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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
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2
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1.3k
views
normalize.AffyBatch.vsn not expressed in vsn
software error vsn affy
7.4 years ago Claudio Lottaz ▴ 40
2
votes
1
reply
1.1k
views
vsn package problem
vsn
updated 8.3 years ago by 65k • written 8.3 years ago by • 0
0
votes
3
replies
2.9k
views
error in vsn package
vsn failure to read documentation error
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 40
1
vote
5
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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
6
replies
2.5k
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
3
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2
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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
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
0
votes
1
reply
1.3k
views
vsn normalization in Ringo package
Normalization vsn Ringo Normalization vsn Ringo
updated 9.7 years ago by ▴ 10 • written 9.8 years ago by ★ 13k
0
votes
1
reply
1.3k
views
VSN with spike-in probes question
vsn vsn
updated 9.8 years ago by ★ 13k • written 9.8 years ago by ▴ 350
0
votes
1
reply
1.3k
views
VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?
vsn PROcess xps vsn PROcess xps
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 350
0
votes
1
reply
1.3k
views
Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
Normalization vsn graph Normalization vsn graph
updated 10.3 years ago by 65k • written 10.3 years ago by ▴ 350
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
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 10.5 years ago by 50k • written 10.5 years ago by ▴ 40
0
votes
0
replies
988
views
question about package AgiMicroRna
Normalization GO vsn Normalization GO vsn
10.7 years ago Guest User ★ 13k
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
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
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
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
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
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0
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943
views
PLS help: is it sound to normalized highthrouput qPCR arrays using vsn?
qPCR Normalization vsn qPCR Normalization vsn
12.0 years ago Ali Mohammadian ▴ 290
0
votes
0
replies
970
views
Problem with BGandNorm() from the Agi4x44PreProcess package
vsn Agi4x44PreProcess vsn Agi4x44PreProcess
12.0 years ago marco fabbri ▴ 320
0
votes
1
reply
1.2k
views
using vsn to normalize protein array data
Microarray vsn Microarray vsn
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 150
0
votes
1
reply
1.2k
views
Problem with BGandNorm() from the Agi4x44PreProcess package
vsn vsn
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ★ 1.4k
0
votes
1
reply
1.3k
views
odd limma results?
vsn limma vsn limma
updated 13.3 years ago by 65k • written 13.3 years ago by ▴ 70
2
votes
4
replies
2.2k
views
limma and minimum fold change
Microarray vsn limma Microarray vsn limma
updated 13.5 years ago by 21k • written 13.5 years ago by ▴ 70
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
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3
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1.5k
views
ChIP-chip sequence bias not removed
Normalization vsn Starr Normalization vsn Starr
updated 13.8 years ago by ▴ 50 • written 13.8 years ago by ▴ 230
0
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4
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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
0
replies
907
views
duplicate spots
vsn vsn
13.9 years ago David ▴ 860
0
votes
1
reply
1.1k
views
No changes between Groups using GeneST Arrays from Affymetrix
GO vsn plier GO vsn plier
updated 14.0 years ago by ▴ 230 • written 14.0 years ago by ▴ 830
0
votes
3
replies
1.1k
views
VSN: minimum number of controls?
Normalization vsn Normalization vsn
updated 14.1 years ago by 25k • written 14.1 years ago by ▴ 20
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
2
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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
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
5
replies
2.9k
views
vsn: meanSdPlot + MAlist
Normalization vsn limma convert Normalization vsn limma convert
updated 14.5 years ago by 25k • written 14.5 years ago by ★ 3.9k
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
1
reply
917
views
multiple Affy normalization results in single object ?
Biobase vsn Biobase vsn
updated 14.7 years ago by 25k • written 14.6 years ago by ▴ 140
0
votes
3
replies
1.5k
views
limma's implementation of VSN
Normalization vsn limma Normalization vsn limma
updated 14.7 years ago by ★ 13k • written 14.7 years ago by ★ 3.9k
0
votes
0
replies
1.3k
views
LIMMA: Why does eBayes expression differ from observed?
Normalization Preprocessing probe vsn limma Normalization Preprocessing probe vsn limma
14.7 years ago Axel Klenk ★ 1.0k
0
votes
0
replies
941
views
Subject: Re: Normalization of arrays where most of the genes change
Normalization vsn limma Normalization vsn limma
15.0 years ago Alicia Oshlack ▴ 70
0
votes
0
replies
1.0k
views
vsn add-on normalization
Normalization vsn Normalization vsn
15.1 years ago Markus Schmidberger ▴ 380
50 results • Page 1 of 1
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Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
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
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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