Showing : gcrma • reset
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Farms library
gcrma PROcess farms gcrma PROcess farms
19.6 years ago Phguardiol@aol.com ▴ 720
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2
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1.5k
views
median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 19.6 years ago by ★ 1.2k • written 19.6 years ago by ▴ 270
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2
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1.7k
views
Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1
affy gcrma matchprobes affyPLM affyio affy gcrma matchprobes affyPLM affyio
updated 19.6 years ago by ▴ 50 • written 19.6 years ago by ▴ 20
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2
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1.1k
views
unnormalised vs normalised distribution
gcrma gcrma
updated 19.6 years ago by ★ 2.2k • written 19.6 years ago by ▴ 830
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8
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2.5k
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error message in gcrma
cdf affy gcrma matchprobes plier cdf affy gcrma matchprobes plier
updated 19.6 years ago by ★ 7.4k • written 19.6 years ago by ▴ 520
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0
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912
views
justGCRMA error in BioC 1.8
Microarray cdf affy gcrma matchprobes Microarray cdf affy gcrma matchprobes
19.6 years ago James W. MacDonald 68k
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0
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1.2k
views
Why mm's changing after bg.adjust.gcrma?
drosgenome1 cdf Biobase reposTools affy gcrma affyPLM simpleaffy affyQCReport affyio cdf
19.7 years ago Jenny Drnevich ★ 2.2k
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4
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2.4k
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Failure to load Biobase
Biobase affy limma gcrma matchprobes affyio Biobase affy limma gcrma matchprobes affyio
updated 19.7 years ago by 25k • written 19.7 years ago by ★ 2.2k
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0
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1.1k
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simpleAffy, custom chip error
GO cdf probe gcrma simpleaffy affyQCReport GO cdf probe gcrma simpleaffy affyQCReport
19.7 years ago Wittner, Ben ▴ 290
0
votes
0
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641
views
Bugfix in gcrma
Microarray Cancer gcrma Microarray Cancer gcrma
19.7 years ago James W. MacDonald 68k
0
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0
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862
views
justGCRMA error in BioC 1.8
cdf affy gcrma matchprobes cdf affy gcrma matchprobes
19.7 years ago echang4@life.uiuc.edu ▴ 110
0
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4
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1.4k
views
a just.gcrma question
gcrma gcrma
updated 19.7 years ago by ▴ 200 • written 19.7 years ago by ▴ 890
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5
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1.7k
views
GCRMA Fold Change
probe gcrma PROcess probe gcrma PROcess
updated 19.7 years ago by ★ 2.2k • written 19.7 years ago by ▴ 20
0
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3
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1.9k
views
error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 19.8 years ago by ▴ 70 • written 19.8 years ago by ★ 2.2k
0
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0
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966
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A questions related to affymetrix chip normalizationfrom multiple platform
hgu133a hgu133b gcrma hgu133a hgu133b gcrma
19.8 years ago Li, Aiguo NIH/NCI ▴ 110
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2
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1.6k
views
AnnBuilder problem for mu11ksuba
Organism mu11ksuba annotate limma gcrma matchprobes annaffy AnnBuilder Organism mu11ksuba
updated 19.8 years ago by ▴ 780 • written 19.8 years ago by ★ 1.4k
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0
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884
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Scaling Factor for Affymetrix chips
affy gcrma simpleaffy affy gcrma simpleaffy
19.9 years ago Jacky Pallas ▴ 10
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1
reply
979
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Scaling Factor for Affymetrix chips.
affy gcrma affy gcrma
updated 19.9 years ago by ▴ 230 • written 19.9 years ago by ▴ 490
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0
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815
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Fwd: Re: Scaling Factor for Affymetrix chips.
GO probe affy gcrma GO probe affy gcrma
19.9 years ago Naomi Altman ★ 6.0k
0
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8
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2.1k
views
Trouble building Bioconductor
gcrma gcrma
19.9 years ago Atro Tossavainen ▴ 160
0
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1
reply
1.2k
views
degraded RNA and background correction
Normalization GO gcrma Normalization GO gcrma
19.9 years ago Jenny Drnevich ★ 2.2k
0
votes
5
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1.8k
views
Problems annotating a gene list
Annotation gcrma Annotation gcrma
updated 19.9 years ago by 21k • written 19.9 years ago by ▴ 110
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2
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1.5k
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Filter on Fold Change
genefilter affy gcrma genefilter affy gcrma
updated 19.9 years ago by ★ 1.0k • written 19.9 years ago by ▴ 110
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6
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2.1k
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 19.9 years ago by 68k • written 19.9 years ago by ▴ 20
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2
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1.0k
views
GCRMA and background
probe affy gcrma probe affy gcrma
updated 19.9 years ago by 68k • written 19.9 years ago by ▴ 460
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3
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1.3k
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GCRMA explained in words
Cancer probe gcrma Cancer probe gcrma
updated 20.0 years ago by ▴ 200 • written 20.0 years ago by ★ 2.0k
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3
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1.3k
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mouse 430_2 error message
gcrma gcrma
updated 20.0 years ago by ▴ 780 • written 20.0 years ago by ▴ 90
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3
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1.4k
views
ad hoc tools for affy tiling arrays?
Normalization Preprocessing gcrma Normalization Preprocessing gcrma
updated 20.0 years ago by ▴ 310 • written 20.0 years ago by ★ 6.5k
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0
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831
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linear model vs. seperate normalization
limma gcrma limma gcrma
20.0 years ago Jianping Jin ▴ 890
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1
reply
859
views
ad hoc tools for affy tiling arrays?
Normalization gcrma Normalization gcrma
updated 20.0 years ago by ▴ 420 • written 20.0 years ago by ▴ 310
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1
reply
1.4k
views
GCRMA
Microarray Preprocessing gcrma BRAIN Microarray Preprocessing gcrma BRAIN
updated 20.0 years ago by ★ 2.0k • written 20.0 years ago by ▴ 20
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3
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975
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comparing method
gcrma gcrma
updated 20.0 years ago by ★ 6.0k • written 20.0 years ago by ▴ 30
0
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0
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1.5k
views
double violation of normalization assumptions?
Microarray Normalization probe limma gcrma Microarray Normalization probe limma gcrma
20.0 years ago Matthew Hannah ▴ 940
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1
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1.7k
views
double violation of normalization assumptions?
Normalization probe limma gcrma Normalization probe limma gcrma
updated 20.0 years ago by ★ 6.0k • written 20.0 years ago by ★ 2.2k
0
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1
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863
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Memory issue on Linux running Affymetrix HG-U133_Plus_2
gcrma gcrma
updated 20.0 years ago by 68k • written 20.0 years ago by ▴ 90
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4
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1.7k
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affy & problems with not enough avaliable memory
affy gcrma affy gcrma
updated 20.0 years ago by ▴ 830 • written 20.0 years ago by ▴ 110
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15
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3.0k
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affy & problems with memory
affy gcrma affy gcrma
updated 20.0 years ago by ▴ 210 • written 20.0 years ago by ▴ 110
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1
reply
856
views
How to cite GCRMA and SAM for paper?
gcrma gcrma
updated 20.0 years ago by ▴ 200 • written 20.0 years ago by ★ 1.1k
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1.2k
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RMA or GCRMA
gcrma gcrma
20.0 years ago Nate King ▴ 30
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1
reply
1.1k
views
GOstats/tkWidgets/gcrma conflict
tkWidgets gcrma matchprobes GOstats tkWidgets gcrma matchprobes GOstats
updated 20.2 years ago by 25k • written 20.2 years ago by ▴ 80
0
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2
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929
views
GCRMA with custom chips
probe gcrma probe gcrma
updated 20.2 years ago by 68k • written 20.2 years ago by ▴ 50
0
votes
1
reply
686
views
gcrma and custom chips
GO probe gcrma GO probe gcrma
updated 20.2 years ago by 68k • written 20.2 years ago by ▴ 50
0
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0
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864
views
E. coli problems: bimodality and gcrma
probe gcrma probe gcrma
20.2 years ago Jenny Drnevich ★ 2.2k
0
votes
1
reply
707
views
bg.adjust.gcrma
cdf affy gcrma cdf affy gcrma
updated 20.3 years ago by 68k • written 20.3 years ago by ▴ 10
0
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0
replies
687
views
System configaration -Bioconductor for the best possible results (in terms of files processed)
gcrma convert gcrma convert
20.3 years ago Chaitanya Kommidi ▴ 30
0
votes
2
replies
1.6k
views
Matchprobe package
cdf probe gcrma cdf probe gcrma
updated 20.4 years ago by ▴ 120 • written 20.4 years ago by ★ 13k
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2
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1.9k
views
gcRMA and normalization
Normalization gcrma Normalization gcrma
updated 20.4 years ago by ▴ 200 • written 20.4 years ago by ▴ 210
0
votes
1
reply
967
views
Problems with justGCRMA: Error in bg.adjust.fullmodel
vsn gcrma matchprobes plier vsn gcrma matchprobes plier
updated 20.4 years ago by 68k • written 20.4 years ago by ▴ 350
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1
reply
2.5k
views
Removing batch effects
vsn gcrma vsn gcrma
updated 20.4 years ago by ▴ 210 • written 20.4 years ago by ▴ 310
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2
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1.2k
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GCRMA, identical normalized values from 3 replicates
affy gcrma affy gcrma
updated 20.4 years ago by ▴ 200 • written 20.4 years ago by ▴ 810
406 results • Page 5 of 9
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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…
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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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