Showing : vsn • reset
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 5.2 years ago by ▴ 70
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
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
4
votes
4
replies
1.6k
views
change all the negative value into positive value
vsn
3.4 years ago yueli7 ▴ 20
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
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
2
votes
3
replies
1.1k
views
one stratum from vsn2
vsn vsn2 onestratum
updated 3.3 years ago by ★ 13k • written 3.3 years ago by • 0
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
1
vote
0
replies
565
views
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
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
1
vote
2
replies
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
2
replies
1.2k
views
Problems encountered using affy in R
Biobase annotate genefilter multtest ROC tkWidgets affy vsn Biobase annotate genefilter
updated 21.2 years ago by 6.7k • written 21.2 years ago by ▴ 20
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
1
reply
690
views
passing marrayRaw data to VSN
vsn vsn
updated 21.1 years ago by ★ 13k • written 21.1 years ago by ▴ 20
0
votes
4
replies
1.2k
views
mas 5.0 presence calls
Microarray Normalization Cancer affy vsn Microarray Normalization Cancer affy vsn
updated 21.3 years ago by ▴ 220 • written 21.3 years ago by ★ 1.4k
0
votes
0
replies
897
views
normalizing affy chips with vsn
Normalization affy vsn Normalization affy vsn
21.3 years ago Oliver Hartmann ▴ 70
0
votes
1
reply
985
views
problem with createBeadSummaryData
Normalization vsn Normalization vsn
updated 15.1 years ago by ★ 1.1k • written 15.1 years ago by ▴ 630
0
votes
0
replies
936
views
Question regarding bg correction/normalization/summarization
Normalization Cancer probe affy vsn plier Normalization Cancer probe affy vsn plier
19.8 years ago Wolfgang Huber ★ 13k
0
votes
2
replies
835
views
Creating an new exprSet
vsn vsn
updated 20.5 years ago by ★ 2.3k • written 20.5 years ago by ▴ 770
0
votes
3
replies
1.1k
views
problem with expresso()
affy vsn affy vsn
updated 21.3 years ago by ★ 13k • written 21.3 years ago by ▴ 70
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
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
1
reply
692
views
vsn and affy
Normalization affy vsn Normalization affy vsn
updated 20.3 years ago by 65k • written 20.3 years ago by ▴ 620
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
0
replies
612
views
Question: Background correction using sequence info!
Normalization vsn gcrma Normalization vsn gcrma
20.1 years ago Puhong Gao ▴ 140
0
votes
1
reply
989
views
data transformation
Normalization vsn codelink Normalization vsn codelink
updated 20.1 years ago by ★ 13k • written 20.1 years ago by ▴ 10
0
votes
0
replies
831
views
gcrma and justRMA
vsn gcrma vsn gcrma
20.1 years ago Arne.Muller@aventis.com ▴ 620
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
0
replies
1.1k
views
technical replicates (again!): a summary
Microarray GO Preprocessing Cancer vsn Microarray GO Preprocessing Cancer vsn
20.1 years ago Ramon Diaz ★ 1.1k
0
votes
1
reply
816
views
Release 1.4 - packages missing?
GO reposTools vsn GO reposTools vsn
updated 19.9 years ago by ★ 3.9k • written 19.9 years ago by ▴ 110
0
votes
1
reply
671
views
Vsn implementation of spot weights
Genetics vsn Genetics vsn
updated 20.6 years ago by ★ 13k • written 20.6 years ago by ▴ 30
0
votes
1
reply
779
views
vsn / rma
Genetics vsn Genetics vsn
updated 21.4 years ago by ★ 13k • written 21.4 years ago by ▴ 30
0
votes
1
reply
1.1k
views
Normalization Recommendations- severe biological variation (from the digest)
Normalization vsn plier Normalization vsn plier
updated 15.8 years ago by ★ 6.0k • written 15.8 years ago by ▴ 20
0
votes
6
replies
1.7k
views
RMA vs VSN
Preprocessing vsn Preprocessing vsn
19.9 years ago Roger Vallejo ▴ 120
0
votes
1
reply
1.1k
views
Problems accessing the Milan package through the vignettes Explorer
Cancer Biobase annotate edd geneplotter multtest tkWidgets affydata vsn graph hexbin
updated 20.9 years ago by ★ 2.9k • written 20.9 years ago by ▴ 130
0
votes
1
reply
988
views
Installation of version 1.4: vsn
vsn vsn
updated 19.9 years ago by ▴ 30 • written 19.9 years ago by ▴ 220
0
votes
1
reply
831
views
vsn problem again...
affy vsn affy vsn
updated 19.9 years ago by 65k • written 19.9 years ago by ▴ 110
0
votes
0
replies
700
views
Re: RMA vs VSN
Normalization Preprocessing Cancer probe affy vsn gcrma Normalization Preprocessing probe
19.8 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
624
views
Question regarding bg correction/normalization/summarization
Normalization affy vsn Normalization affy vsn
19.8 years ago Tova Fuller ▴ 10
0
votes
1
reply
937
views
number of affy-chips needed to fit rma model
vsn vsn
updated 19.8 years ago by ★ 2.3k • written 19.8 years ago by ▴ 430
0
votes
1
reply
878
views
VSN combined with RMA
Normalization vsn Normalization vsn
updated 19.8 years ago by ★ 2.3k • written 19.8 years ago by ▴ 90
0
votes
0
replies
1.1k
views
vsn vs quantiles, bimodal data
Normalization vsn codelink Normalization vsn codelink
19.7 years ago Rohit Ghai ▴ 80
0
votes
3
replies
959
views
VSN error : 'ny' does not seem to be resulting from vsn
vsn vsn
updated 19.5 years ago by ★ 13k • written 19.5 years ago by ★ 1.1k
0
votes
0
replies
596
views
function log.na() removed from package vsn >= 1.5.1
vsn marray vsn marray
19.5 years ago Wolfgang Huber ★ 13k
0
votes
1
reply
1.2k
views
normalizaton between studies
Normalization vsn DOSE Normalization vsn DOSE
updated 19.4 years ago by ▴ 10 • written 19.4 years ago by ▴ 620
0
votes
3
replies
1.3k
views
vsn in limma or marray/arrayMagic
Normalization vsn limma marray Normalization vsn limma marray
19.3 years ago A.E.Schiel@lumc.nl ▴ 100
0
votes
2
replies
1.0k
views
normalizeQuantiles : log2 or not??
Normalization vsn Normalization vsn
19.2 years ago Marcelo Luiz de Laia ▴ 770
0
votes
2
replies
1.1k
views
help in arrayMagic?
vsn vsn
updated 19.1 years ago by ▴ 40 • written 19.1 years ago by ▴ 30
0
votes
2
replies
813
views
Error loading some BioC packages !
vsn vsn
updated 19.0 years ago by ★ 7.4k • written 19.0 years ago by ▴ 540
0
votes
0
replies
1.2k
views
Bioconductor 1.2 Released
Microarray SAGE Normalization GO GUI Cancer cdf affy vsn graph AnnBuilder Microarray
20.9 years ago Jeff Gentry ★ 3.9k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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