Showing : assign • reset
0
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3
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1.0k
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gcrma problem
Microarray Cancer probe gcrma ASSIGN Microarray Cancer probe gcrma ASSIGN
updated 19.1 years ago by 65k • written 19.1 years ago by ▴ 120
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3
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2.5k
views
heatmap.2
ASSIGN ASSIGN
updated 15.4 years ago by 21k • written 15.4 years ago by ▴ 10
0
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3
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1.4k
views
LimmaGUI Error
Normalization GO limmaGUI ASSIGN Normalization GO limmaGUI ASSIGN
18.8 years ago Brooke-Powell, Elizabeth ▴ 170
0
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3
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1.0k
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comparing data frames
affy ASSIGN affy ASSIGN
updated 20.0 years ago by ★ 1.8k • written 20.0 years ago by ▴ 300
0
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5
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1.9k
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Question regarding cellhts2 output
Normalization Visualization PROcess cellHTS2 ASSIGN Normalization Visualization PROcess
11.1 years ago • updated 11.0 years ago maziz@tgen.org ▴ 70
0
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4
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1.5k
views
edgeR: design matrix
ASSIGN ASSIGN
updated 11.9 years ago by 50k • written 11.9 years ago by ▴ 420
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3
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1.3k
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working with two factors in DESeq to analyze RNA-seq
DESeq ASSIGN DESeq ASSIGN
updated 13.2 years ago by 50k • written 13.2 years ago by ▴ 150
0
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3
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988
views
HTqPCR and limma and factorial design with no replicates
Microarray qPCR Classification limma HTqPCR ASSIGN Microarray qPCR Classification limma
updated 14.2 years ago by ★ 6.0k • written 14.3 years ago by ▴ 810
0
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11
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1.8k
views
...another question about using weights on microarray analysis
Microarray limma ASSIGN Microarray limma ASSIGN
15.2 years ago Erika Melissari ▴ 250
0
votes
8
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3.1k
views
Annotation files for bacterial genome RNAseq
Alignment Annotation ASSIGN Alignment Annotation ASSIGN
updated 9.9 years ago by 65k • written 9.9 years ago by ▴ 80
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2
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768
views
modify CDF file for array study
cdf probe affy ASSIGN cdf probe affy ASSIGN
updated 16.5 years ago by ▴ 120 • written 16.5 years ago by ▴ 10
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4
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1.5k
views
problem in reading bam files with EDASeq
Rsamtools EDASeq ASSIGN Rsamtools EDASeq ASSIGN
updated 12.3 years ago by ▴ 950 • written 12.3 years ago by ▴ 500
0
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8
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2.9k
views
biomaRt - batch query for chromosome location to gene identifier?
biomaRt ASSIGN biomaRt ASSIGN
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 120
0
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2
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1.3k
views
error/problem with biomaRt gene symbol query
Microarray Cancer probe biomaRt ASSIGN Microarray Cancer probe biomaRt ASSIGN
updated 13.8 years ago by ▴ 500 • written 13.8 years ago by ▴ 100
0
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2
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844
views
spot weight in limma
oligo ASSIGN oligo ASSIGN
19.5 years ago Ren Na ▴ 250
0
votes
4
replies
3.5k
views
edgeR : input and design matrix help
edgeR ASSIGN edgeR ASSIGN
12.0 years ago KJ Lim ▴ 420
0
votes
2
replies
955
views
Creating a customized cut flow with the affy/limma packages
GO limma ASSIGN GO limma ASSIGN
updated 12.2 years ago by 65k • written 12.2 years ago by ▴ 20
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votes
12
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2.1k
views
Newbie methylation and stats question
probe ASSIGN probe ASSIGN
updated 11.9 years ago by ★ 4.2k • written 11.9 years ago by ▴ 440
0
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4
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1.5k
views
GenomicRanges select parameter
GenomicRanges ASSIGN GenomicRanges ASSIGN
updated 9.9 years ago by ▴ 30 • written 9.9 years ago by ★ 11k
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5
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4.3k
views
annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 9.8 years ago by 65k • written 9.8 years ago by ▴ 70
0
votes
3
replies
1.2k
views
mogene10stprobeset.db error
Normalization ASSIGN Normalization ASSIGN
updated 13.8 years ago by 6.7k • written 13.8 years ago by ▴ 170
0
votes
2
replies
951
views
Limma and limmaGUI with Imagene files, problems/bugs report
limma limmaGUI ASSIGN limma limmaGUI ASSIGN
updated 19.4 years ago by 50k • written 19.4 years ago by ▴ 50
0
votes
2
replies
1.2k
views
DEseq
ASSIGN ASSIGN
updated 12.2 years ago by ★ 6.0k • written 12.2 years ago by ▴ 30
0
votes
2
replies
1.0k
views
LIMMA: how to assign file name
limma ASSIGN limma ASSIGN
updated 5.3 years ago by 0 • written 19.0 years ago by ▴ 180
0
votes
2
replies
1.5k
views
Limma: Extract genes from decideTests result
limma ASSIGN limma ASSIGN
updated 18.2 years ago by ▴ 100 • written 18.2 years ago by ▴ 360
1
vote
3
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1.3k
views
Limma and Names Assignment
ASSIGN ASSIGN
written 12.6 years ago by ▴ 760
0
votes
11
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3.5k
views
SNP6 data to VCF
SNP oligo ASSIGN SNP oligo ASSIGN
updated 5.6 years ago by • 0 • written 12.2 years ago by 21k
0
votes
2
replies
1.4k
views
Question regarding cellhts2 output
Normalization cellHTS2 ASSIGN Normalization cellHTS2 ASSIGN
11.8 years ago maziz@tgen.org ▴ 70
0
votes
3
replies
1.1k
views
Integrating Codelink data with bioconductor (using affy and limmafunctions)
Microarray Annotation Normalization affy limma PROcess codelink ASSIGN Microarray affy
updated 19.0 years ago by ▴ 760 • written 19.0 years ago by 50k
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votes
1
reply
3.6k
views
how deal with multiplicate affy probes?
Alignment mgu74av2 probe affy ASSIGN Alignment mgu74av2 probe affy ASSIGN
updated 20.0 years ago by ★ 5.5k • written 20.0 years ago by ▴ 50
0
votes
1
reply
1.3k
views
Bootstrapping paired samples and tiny groups
ASSIGN ASSIGN
updated 13.6 years ago by ★ 6.0k • written 13.6 years ago by ▴ 830
0
votes
1
reply
777
views
single channel analysis
Annotation Normalization limma ASSIGN Annotation Normalization limma ASSIGN
updated 14.0 years ago by ▴ 860 • written 14.0 years ago by ▴ 720
0
votes
2
replies
976
views
single channel analysis
Annotation ASSIGN Annotation ASSIGN
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 860
0
votes
1
reply
1.2k
views
loop over IRanges spaces
Coverage convert rtracklayer ASSIGN Coverage convert rtracklayer ASSIGN
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ▴ 60
0
votes
1
reply
632
views
Please help: AffylmGUI errors
Microarray affylmGUI ASSIGN Microarray affylmGUI ASSIGN
updated 19.2 years ago by ★ 7.4k • written 19.2 years ago by ▴ 30
0
votes
2
replies
970
views
gene classification problem
GO affy ASSIGN GO affy ASSIGN
updated 19.4 years ago by ▴ 290 • written 19.4 years ago by ▴ 890
0
votes
1
reply
1.5k
views
Seeking assistance on ROC
Microarray GO Classification ROC graph ASSIGN Microarray GO Classification ROC graph
updated 14.3 years ago by ★ 13k • written 14.3 years ago by 21k
0
votes
1
reply
904
views
Multiple genes per probeset
Annotation Cancer mouse4302 annaffy ASSIGN Annotation Cancer mouse4302 annaffy ASSIGN
updated 14.0 years ago by 65k • written 14.0 years ago by ★ 2.0k
0
votes
3
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1.3k
views
Question about clustering and cluster validation
ASSIGN ASSIGN
updated 13.5 years ago by ▴ 20 • written 13.5 years ago by ▴ 370
0
votes
3
replies
1.7k
views
Fwd: Re: which package can do GSEA for no model organism
Annotation GO Organism ASSIGN Annotation GO Organism ASSIGN
updated 14.8 years ago by ▴ 40 • written 14.8 years ago by ▴ 340
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2
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2.0k
views
Outputting dendrogram with large numbers of genes without losing resolution
ASSIGN ASSIGN
updated 16.8 years ago by 21k • written 16.8 years ago by ▴ 40
0
votes
2
replies
888
views
How to permute the CEL files
ASSIGN ASSIGN
updated 14.9 years ago by 25k • written 14.9 years ago by ▴ 840
0
votes
1
reply
1.2k
views
Changes in siggenes?
Prostate hgu133a2 probe affy siggenes ASSIGN Prostate hgu133a2 probe affy siggenes
updated 14.3 years ago by ▴ 900 • written 14.3 years ago by ▴ 10
0
votes
1
reply
974
views
Array normalisation with Limma: would this be reasonable?
ASSIGN ASSIGN
17.4 years ago J.delasHeras@ed.ac.uk ★ 1.9k
0
votes
1
reply
931
views
Re: order in affy for R
probe affy ASSIGN probe affy ASSIGN
updated 21.9 years ago by ▴ 640 • written 21.9 years ago by ★ 2.3k
0
votes
1
reply
1.3k
views
simpleaffy 2.14.02, setQCEnvironment
cdf simpleaffy ASSIGN cdf simpleaffy ASSIGN
updated 16.6 years ago by ★ 1.1k • written 16.6 years ago by ▴ 50
0
votes
2
replies
965
views
Single Channel Approach for Agilent Arrays
limma ASSIGN limma ASSIGN
updated 17.6 years ago by ★ 6.0k • written 17.6 years ago by ▴ 100
0
votes
1
reply
1.6k
views
Problems with url/download and http_proxy
Biobase annotate edd geneplotter tkWidgets ASSIGN Biobase annotate edd geneplotter
updated 21.9 years ago by ▴ 50 • written 21.9 years ago by ▴ 460
0
votes
1
reply
785
views
mean of individual rows for subsets of columns in an ExprSet
ASSIGN ASSIGN
updated 20.7 years ago by 6.7k • written 20.7 years ago by ▴ 280
0
votes
1
reply
815
views
[R-SIG-Mac] trouble running Bioconductor
limma BUS ASSIGN limma BUS ASSIGN
updated 17.7 years ago by ★ 7.4k • written 17.7 years ago by ▴ 430
50 results • Page 1 of 1
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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. …
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
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Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
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Scholar to James W. MacDonald 65k
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