Showing : marray • reset
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Problems with BioConductor
marray marray
updated 21.4 years ago by ★ 3.9k • written 21.4 years ago by ▴ 10
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936
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Flagging spots (was: Bioconductor documentation
Normalization limma marray Normalization limma marray
21.4 years ago Gordon Smyth 53k
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4
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1.6k
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problem reading genepix files using both marray andlimma functions
limma marray limma marray
updated 21.4 years ago by ▴ 60 • written 21.4 years ago by ★ 3.4k
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1.7k
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problem reading genepix files using both marray and limma functions
limma marray limma marray
updated 21.4 years ago by 53k • written 21.4 years ago by ▴ 60
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1.1k
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Normalization with marray on technical replicates
Normalization Cancer marray Normalization Cancer marray
updated 21.5 years ago by ▴ 920 • written 21.5 years ago by ★ 2.0k
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1.1k
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read.marrayRaw()
marray ASSIGN marray ASSIGN
updated 21.5 years ago by ▴ 920 • written 21.5 years ago by ▴ 130
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992
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marray error message
marray marray
updated 21.5 years ago by ▴ 90 • written 21.5 years ago by ▴ 320
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859
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marray or marrayClasses and others?
marray marray
updated 21.6 years ago by ▴ 920 • written 21.6 years ago by ▴ 10
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1.1k
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bug in maNormMain ?
Normalization marray Normalization marray
updated 21.7 years ago by ★ 3.9k • written 21.7 years ago by ▴ 100
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841
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Normalization of Intensities
gcrma marray gcrma marray
21.7 years ago Naomi Altman ★ 6.0k
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import cDNA microarray data into R
marray marray
updated 21.7 years ago by ▴ 920 • written 21.7 years ago by ▴ 10
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1.2k
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reading .gpr w/limma - error (bug??)
marray marray
21.7 years ago Mayte Suarez-Farinas ▴ 300
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1.1k
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Bug in marray???
marray marray
updated 21.7 years ago by ▴ 920 • written 21.7 years ago by ▴ 40
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3
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1.5k
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Confusion for choosing package for microarray data analysis
Microarray limma siggenes marray Microarray limma siggenes marray
updated 21.9 years ago by ▴ 140 • written 21.9 years ago by ▴ 60
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problem for dealing with replicated spots in slide
Microarray marray Microarray marray
updated 21.9 years ago by 53k • written 21.9 years ago by ▴ 60
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1.8k
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normalization data with ..txt or ..xls file by marray or limma
Normalization limma marray Normalization limma marray
21.9 years ago Matthew Ritchie ▴ 1000
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886
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normalization data with ..txt or ..xls file by marray or limma
Microarray Normalization limma marray Microarray Normalization limma marray
21.9 years ago rwin qian ▴ 50
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6
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1.8k
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(no subject)
marray marray
updated 21.9 years ago by 68k • written 21.9 years ago by ▴ 200
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1.9k
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M vs A plot
Microarray Normalization Regression Cancer marray Microarray Normalization Regression
updated 21.9 years ago by ★ 6.0k • written 22.0 years ago by ★ 2.0k
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1.7k
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Reading data from SMD database
marray marray
updated 21.9 years ago by ▴ 310 • written 21.9 years ago by ▴ 220
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903
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marrayClasses packages
marray marray
21.9 years ago Gu, Joyce ▴ 20
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970
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t test
Microarray marray Microarray marray
22.0 years ago Binita Dutta ▴ 100
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Re: [Fwd: Bioc Book Chapter] (Gordon K Smyth) Biocondu ctor Digest, Vol 11, Issue 38
Microarray Preprocessing limma marray convert oligo Microarray Preprocessing limma marray
22.0 years ago michael watson IAH-C ★ 3.4k
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Re: [Fwd: Bioc Book Chapter] (Gordon K Smyth) Bioconductor Digest, Vol 11, Issue 38
Microarray Preprocessing limma marray convert oligo Microarray Preprocessing limma marray
22.0 years ago Christopher Wilkinson ▴ 140
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3
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2.3k
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RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
written 22.0 years ago by ▴ 70
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5
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1.8k
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Problem with read.marrayRaw
marray marray
updated 22.0 years ago by ▴ 80 • written 22.0 years ago by ▴ 200
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1.2k
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Problem with marray
marray marray
22.0 years ago Patrice Godard ▴ 20
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4
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1.4k
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[maNorm] Normalization a complex experiment...
Normalization limma marray Normalization limma marray
updated 22.0 years ago by 53k • written 22.0 years ago by ▴ 770
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806
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Read ImaGene output files...
limma marray limma marray
updated 22.1 years ago by 53k • written 22.1 years ago by ▴ 150
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971
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Agilent data Normalization
Normalization GO marray Normalization GO marray
22.1 years ago Joel Parker ▴ 10
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911
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MA plots without bg correction (mArray)
marray marray
updated 22.1 years ago by ▴ 920 • written 22.1 years ago by ▴ 40
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2
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1.1k
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Help for make a dendrogram (philogenetic tree)
limma marray limma marray
updated 22.1 years ago by 53k • written 22.1 years ago by ▴ 770
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784
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Help for make a dendrogram (philogenetic tree)
limma marray limma marray
22.1 years ago Marcelo Luiz de Laia ▴ 770
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2
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1.0k
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More than one weight with marrayRaw class
marray marray
updated 22.2 years ago by 53k • written 22.2 years ago by ▴ 90
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1.6k
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using marrayInput package with GenePix .gpr file - read.GenePix()
GO marray GO marray
updated 22.2 years ago by ▴ 920 • written 22.2 years ago by ▴ 10
135 results • Page 3 of 3
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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Teacher to Gordon Smyth 53k
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