Showing : vsn • reset
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
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
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
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 17.5 years ago by ★ 2.9k
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
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
6
replies
1.7k
views
RMA vs VSN
Preprocessing vsn Preprocessing vsn
19.9 years ago Roger Vallejo ▴ 120
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
8.7 years ago • updated 8.6 years ago guojiegina • 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
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
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
5
replies
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
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
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
5
replies
1.5k
views
Detection of differential expression using limma
Microarray Normalization vsn limma Microarray Normalization vsn limma
updated 15.6 years ago by ▴ 10 • written 15.6 years ago by ▴ 60
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
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
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
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
4
replies
1.1k
views
VSN exclusion of probes
probe vsn oligo probe vsn oligo
updated 17.4 years ago by ★ 13k • written 17.4 years ago by ▴ 330
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
4
votes
4
replies
1.7k
views
change all the negative value into positive value
vsn
3.4 years ago yueli7 ▴ 20
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
4
replies
1.1k
views
VSN 2.2
Normalization vsn Normalization vsn
updated 17.0 years ago by ★ 13k • written 17.0 years ago by ▴ 330
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
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
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
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
3
replies
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
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
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
0
votes
3
replies
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
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
3
replies
960
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
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
0
votes
3
replies
1.2k
views
Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
probe annotate geneplotter affy vsn Ringo probe annotate geneplotter affy vsn Ringo
updated 15.8 years ago by ▴ 730 • written 15.8 years ago by ▴ 110
0
votes
3
replies
1.1k
views
vsn with a reference set
vsn PROcess vsn PROcess
updated 16.1 years ago by ★ 13k • written 16.1 years ago by ▴ 110
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
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
3
replies
2.5k
views
Error: could not find function "normalize.AffyBatch.vsn"
vsn
updated 7.3 years ago by 65k • written 7.3 years ago by • 0
0
votes
3
replies
1.1k
views
problem with vsn and affy data...
affy vsn affy vsn
updated 21.4 years ago by ★ 1.0k • written 21.4 years ago by ▴ 70
0
votes
3
replies
872
views
vsn2 bug?
Microarray Normalization vsn Microarray Normalization vsn
updated 16.9 years ago by ★ 13k • written 16.9 years ago by ▴ 430
0
votes
3
replies
969
views
quality data check
affy vsn limma affy vsn limma
updated 19.0 years ago by 21k • written 19.0 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
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
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
1.2k
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
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
2
replies
818
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
2
replies
1.1k
views
help in arrayMagic?
vsn vsn
updated 19.1 years ago by ▴ 40 • written 19.1 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
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Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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