Showing : assign • reset
0
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
votes
11
replies
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
11
replies
3.5k
views
SNP6 data to VCF
SNP oligo ASSIGN SNP oligo ASSIGN
updated 5.7 years ago by • 0 • written 12.2 years ago by 21k
0
votes
9
replies
2.8k
views
Conversion of affymetrix cell file to raw text file
Microarray probe ASSIGN Microarray probe ASSIGN
13.4 years ago viritha kaza ▴ 580
0
votes
8
replies
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
votes
8
replies
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
0
votes
5
replies
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
5
replies
1.9k
views
Question regarding cellhts2 output
Normalization Visualization PROcess cellHTS2 ASSIGN Normalization Visualization PROcess
11.1 years ago maziz@tgen.org ▴ 70
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
2.2k
views
yieldSize and paired end data in SummarizeOverlaps error?
BSgenome PROcess BSgenome ASSIGN BSgenome PROcess BSgenome ASSIGN
updated 11.1 years ago by ★ 6.8k • written 11.2 years ago by ▴ 10
0
votes
4
replies
1.5k
views
GenomicRanges select parameter
GenomicRanges ASSIGN GenomicRanges ASSIGN
updated 9.9 years ago by ▴ 30 • written 9.9 years ago by ★ 11k
0
votes
4
replies
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
votes
4
replies
1.5k
views
edgeR: design matrix
ASSIGN ASSIGN
updated 11.9 years ago by 50k • written 12.0 years ago by ▴ 420
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
4
replies
1.1k
views
BlueFuse in limmaGUI [was LimmaGUI Error]
Normalization GO limmaGUI ASSIGN Normalization GO limmaGUI ASSIGN
updated 18.8 years ago by ▴ 170 • written 18.8 years ago by 50k
0
votes
3
replies
1.0k
views
comparing data frames
affy ASSIGN affy ASSIGN
updated 20.0 years ago by ★ 1.8k • written 20.0 years ago by ▴ 300
0
votes
3
replies
1.0k
views
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
0
votes
3
replies
1.2k
views
Dealing with probes with high fold change but PA call 0
Clustering probe ASSIGN Clustering probe ASSIGN
updated 10.4 years ago by ★ 13k • written 10.4 years ago by ▴ 230
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
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
1
vote
3
replies
1.3k
views
Limma and Names Assignment
ASSIGN ASSIGN
written 12.6 years ago by ▴ 760
0
votes
3
replies
992
views
HTqPCR and limma and factorial design with no replicates
Microarray qPCR Classification limma HTqPCR ASSIGN Microarray qPCR Classification limma
updated 14.3 years ago by ★ 6.0k • written 14.3 years ago by ▴ 810
0
votes
3
replies
2.5k
views
heatmap.2
ASSIGN ASSIGN
updated 15.4 years ago by 21k • written 15.4 years ago by ▴ 10
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 14.9 years ago by ▴ 40 • written 14.9 years ago by ▴ 340
0
votes
3
replies
1.4k
views
LimmaGUI Error
Normalization GO limmaGUI ASSIGN Normalization GO limmaGUI ASSIGN
18.8 years ago Brooke-Powell, Elizabeth ▴ 170
0
votes
3
replies
1.3k
views
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
votes
3
replies
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
2
replies
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
votes
2
replies
978
views
single channel analysis
Annotation ASSIGN Annotation ASSIGN
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 860
0
votes
2
replies
1.2k
views
error on detecting regions
ASSIGN ASSIGN
updated 9.9 years ago by ▴ 440 • written 9.9 years ago by ★ 13k
0
votes
2
replies
771
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
0
votes
2
replies
972
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
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
2
replies
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
892
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
2
replies
966
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
2
replies
907
views
reference argument in limma factorial design
Microarray limma ASSIGN Microarray limma ASSIGN
updated 15.3 years ago by ★ 6.0k • written 15.3 years ago by 50k
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
0
votes
2
replies
1.2k
views
htSeqTools - naming RangedData objects?
htSeqTools ASSIGN htSeqTools ASSIGN
updated 12.3 years ago by ★ 11k • written 12.3 years ago by ▴ 70
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
0
votes
2
replies
1.2k
views
DEseq
ASSIGN ASSIGN
updated 12.2 years ago by ★ 6.0k • written 12.3 years ago by ▴ 30
0
votes
2
replies
852
views
spot weight in limma
oligo ASSIGN oligo ASSIGN
19.5 years ago Ren Na ▴ 250
0
votes
2
replies
1.1k
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
954
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
limma single-channel analysis and intraspotCorrelation
GO limma ASSIGN GO limma ASSIGN
updated 19.5 years ago by 50k • written 19.5 years ago by ▴ 250
0
votes
2
replies
1.6k
views
plotting probes along a chromosome
graph GenomeGraphs ASSIGN graph GenomeGraphs ASSIGN
updated 12.8 years ago by ▴ 550 • written 12.8 years ago by ▴ 240
0
votes
2
replies
3.6k
views
From location to get the SNP rs ID
SNP Cancer SNPlocs ASSIGN SNP Cancer SNPlocs ASSIGN
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 970
0
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 13.7 years ago by ▴ 830
0
votes
1
reply
778
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
50 results • Page 1 of 1
Recent ...
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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