Showing : vsn • reset
1
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308
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
8 months ago Arend ▴ 10
0
votes
3
replies
1.7k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
0
votes
5
replies
833
views
In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 2.1 years ago by 48k • written 2.1 years ago by • 0
2
votes
3
replies
819
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one stratum from vsn2
vsn vsn2 onestratum
updated 2.7 years ago by 13k • written 2.7 years ago by • 0
4
votes
4
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1.3k
views
change all the negative value into positive value
vsn
2.8 years ago yueli7 ▴ 20
7
votes
3
replies
3.6k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 10 months ago by 48k • written 4.6 years ago by ▴ 70
4
votes
4
replies
1.3k
views
Where can I use the VSN source code in C++?
vsn r language C++ source code
updated 6.6 years ago by ▴ 720 • written 6.6 years ago by • 0
1
vote
2
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1.1k
views
Bug in vsn2 in package vsn?
vsn vsn2
updated 6.6 years ago by 13k • written 6.6 years ago by ★ 2.8k
0
votes
3
replies
2.3k
views
Error: could not find function "normalize.AffyBatch.vsn"
vsn
updated 6.7 years ago by 63k • written 6.7 years ago by • 0
0
votes
2
replies
1.2k
views
normalize.AffyBatch.vsn not expressed in vsn
software error vsn affy
6.8 years ago Claudio Lottaz ▴ 40
2
votes
1
reply
924
views
vsn package problem
vsn
updated 7.7 years ago by 63k • written 7.7 years ago by • 0
0
votes
3
replies
2.6k
views
error in vsn package
vsn failure to read documentation error
updated 7.9 years ago by 13k • written 7.9 years ago by ▴ 40
1
vote
5
replies
1.3k
views
normalization of a miRNA microarray
normalization vsn eximir microarray miRNA
updated 8.0 years ago by 13k • written 8.0 years ago by ▴ 50
0
votes
6
replies
2.2k
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
8.1 years ago • updated 8.0 years ago guojiegina • 0
3
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2
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5.4k
views
problem installing "vsn" on debian... gcc: error: unrecognized command line option -fstack-protector-strong
install vsn gcc debian
8.6 years ago regcl • 0
5
votes
6
replies
5.7k
views
proper transformation for differential expression in normalized log expression data
tcga rnaseq deseq2 vsn edger
updated 8.7 years ago by 48k • written 8.7 years ago by • 0
0
votes
1
reply
1.1k
views
vsn normalization in Ringo package
Normalization vsn Ringo Normalization vsn Ringo
updated 9.2 years ago by ▴ 10 • written 9.2 years ago by ★ 12k
0
votes
1
reply
1.1k
views
VSN with spike-in probes question
vsn vsn
updated 9.3 years ago by 13k • written 9.3 years ago by ▴ 350
0
votes
1
reply
1.1k
views
VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?
vsn PROcess xps vsn PROcess xps
updated 9.6 years ago by 13k • written 9.6 years ago by ▴ 350
0
votes
1
reply
1.2k
views
Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
Normalization vsn graph Normalization vsn graph
updated 9.7 years ago by 63k • written 9.7 years ago by ▴ 350
0
votes
1
reply
2.0k
views
Importing RMA processed data into limma for eBayes
Microarray Normalization affy vsn limma PROcess xps Microarray Normalization affy vsn
9.8 years ago Matthew Thornton ▴ 350
0
votes
5
replies
2.0k
views
Single-channel GenePix analysis with Limma (bg correction, normalization, weights)
Microarray Normalization vsn limma ASSIGN Microarray Normalization vsn limma ASSIGN
updated 9.9 years ago by 48k • written 9.9 years ago by ▴ 40
0
votes
0
replies
877
views
question about package AgiMicroRna
Normalization GO vsn Normalization GO vsn
10.1 years ago Guest User ★ 12k
0
votes
0
replies
1.5k
views
Bioconductor Digest, Vol 121, Issue 29
miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn
10.5 years ago Matthew Thornton ▴ 350
0
votes
6
replies
1.5k
views
Heatmaps for Agilent Single Color 4x44k using limma and vsn.
Annotation Normalization vsn limma Annotation Normalization vsn limma
updated 10.5 years ago by 63k • written 10.5 years ago by ▴ 50
0
votes
8
replies
1.9k
views
vsn preprocess with oligo package
vsn oligo oligoClasses vsn oligo oligoClasses
updated 10.7 years ago by 63k • written 10.7 years ago by ▴ 110
0
votes
3
replies
1.3k
views
Most diff exp genes are up-regulated... can this be true?
Microarray Normalization vsn limma siggenes Microarray Normalization vsn limma siggenes
10.8 years ago Peter Davidsen ▴ 210
0
votes
2
replies
1.4k
views
normalize.AffyBatch.vsn with reference vsn object
vsn vsn
updated 11.4 years ago by 13k • written 11.4 years ago by ▴ 30
0
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0
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836
views
PLS help: is it sound to normalized highthrouput qPCR arrays using vsn?
qPCR Normalization vsn qPCR Normalization vsn
11.5 years ago Ali Mohammadian ▴ 290
0
votes
0
replies
854
views
Problem with BGandNorm() from the Agi4x44PreProcess package
vsn Agi4x44PreProcess vsn Agi4x44PreProcess
11.5 years ago marco fabbri ▴ 320
0
votes
1
reply
1.1k
views
using vsn to normalize protein array data
Microarray vsn Microarray vsn
updated 12.0 years ago by 13k • written 12.0 years ago by ▴ 150
0
votes
1
reply
1.0k
views
Problem with BGandNorm() from the Agi4x44PreProcess package
vsn vsn
updated 12.4 years ago by 13k • written 12.4 years ago by ★ 1.4k
0
votes
1
reply
1.1k
views
odd limma results?
vsn limma vsn limma
updated 12.7 years ago by 63k • written 12.7 years ago by ▴ 70
2
votes
4
replies
2.0k
views
limma and minimum fold change
Microarray vsn limma Microarray vsn limma
updated 12.9 years ago by 21k • written 12.9 years ago by ▴ 70
0
votes
1
reply
1.6k
views
Question: How does limma derives its logFC value in two colored arrays?
Yeast affy vsn limma Yeast affy vsn limma
updated 13.0 years ago by ▴ 350 • written 13.0 years ago by 48k
0
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3
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1.3k
views
ChIP-chip sequence bias not removed
Normalization vsn Starr Normalization vsn Starr
updated 13.2 years ago by ▴ 50 • written 13.2 years ago by ▴ 230
0
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4
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1.5k
views
gc-rma and vsn normalization for rat microarray data
Microarray Annotation Normalization vsn bgx puma Microarray Annotation Normalization vsn
updated 13.3 years ago by ★ 4.3k • written 13.3 years ago by ▴ 60
0
votes
0
replies
776
views
duplicate spots
vsn vsn
13.3 years ago David ▴ 860
0
votes
1
reply
967
views
No changes between Groups using GeneST Arrays from Affymetrix
GO vsn plier GO vsn plier
updated 13.5 years ago by ▴ 230 • written 13.5 years ago by ▴ 830
0
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3
replies
999
views
VSN: minimum number of controls?
Normalization vsn Normalization vsn
updated 13.5 years ago by 25k • written 13.5 years ago by ▴ 20
0
votes
6
replies
1.6k
views
Normalisation of Agilent microRNA arrays using inbuilt controls?
GO Cancer vsn AgiMicroRna GO Cancer vsn AgiMicroRna
updated 13.6 years ago by ★ 3.5k • written 13.6 years ago by ★ 1.9k
0
votes
2
replies
1.4k
views
MA plots + dye swap
Normalization vsn limma Normalization vsn limma
updated 13.7 years ago by ▴ 340 • written 13.7 years ago by ★ 3.7k
0
votes
2
replies
1.3k
views
vsn and oligo (or xps?) packages for GeneST expression arrays
vsn oligo xps vsn oligo xps
updated 13.8 years ago by ★ 3.9k • written 13.8 years ago by ▴ 270
0
votes
5
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2.5k
views
vsn: meanSdPlot + MAlist
Normalization vsn limma convert Normalization vsn limma convert
updated 13.9 years ago by 25k • written 13.9 years ago by ★ 3.7k
0
votes
11
replies
2.7k
views
Very low P-values in limma
miRNA Microarray Normalization GO vsn limma microRNA miRNA Microarray Normalization GO
updated 14.0 years ago by ★ 1.3k • written 14.0 years ago by 48k
0
votes
1
reply
784
views
multiple Affy normalization results in single object ?
Biobase vsn Biobase vsn
updated 14.1 years ago by 25k • written 14.1 years ago by ▴ 140
0
votes
3
replies
1.3k
views
limma's implementation of VSN
Normalization vsn limma Normalization vsn limma
updated 14.1 years ago by 13k • written 14.1 years ago by ★ 3.7k
0
votes
0
replies
1.1k
views
LIMMA: Why does eBayes expression differ from observed?
Normalization Preprocessing probe vsn limma Normalization Preprocessing probe vsn limma
14.2 years ago Axel Klenk ▴ 990
0
votes
0
replies
804
views
Subject: Re: Normalization of arrays where most of the genes change
Normalization vsn limma Normalization vsn limma
14.4 years ago Alicia Oshlack ▴ 70
0
votes
0
replies
902
views
vsn add-on normalization
Normalization vsn Normalization vsn
14.5 years ago Markus Schmidberger ▴ 380
50 results • Page 1 of 1
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Replies
Answer: Gviz: UcscTrack and "GC Percent" information by Daniel E. Weeks ▴ 20
**Answer** In https://github.com/ivanek/Gviz/issues/71 an update that fixes this issue was documented - there it is stated that "…
Comment: Biostrings error at retrieving protein sequences by James W. MacDonald 63k
It depends on what kind of whitespace it is. If the whitespace is just a space, then it will work. But if it's a tab, it won't. ``` > gsub…
Comment: Biostrings error at retrieving protein sequences by nromerov • 0
If i write it like ```r gsub(" .*", "", names(protein_sequences)) ``` it will delet all the extra information if it is on the AAString…
Comment: bug in block.plsda from mixOmics? by Lluís Revilla Sancho ▴ 720
Oh, sorry for the noise, I see that just after Bioconductor 3.16 the bug is fixed in both 3.17 and in devel. Thanks for checking.
Answer: Mixed up sample info with plotPCA by Michael Love 40k
I can already tell there is code you aren't showing. For example, your `pcaData` has a variable 'group' that isn't in the previous sample i…
Votes
Answer: Mouse to Human Genes using bioconductor
Mouse to Human Genes using bioconductor
Answer: Biostrings error at retrieving protein sequences
Answer: Biostrings error at retrieving protein sequences
Answer: How do I merge a list of GRanges?
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