Showing : illumina • reset
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
8.9 years ago • updated 8.8 years ago svlachavas ▴ 830
4
votes
8
replies
10k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 10
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
0
votes
2
replies
5.3k
views
How to read bgx files in R
microarray annotation illumina
8.8 years ago kanacska ▴ 10
4
votes
2
replies
4.6k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 100
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
8.1 years ago rasii • 0
0
votes
6
replies
4.0k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina normalization microarray
updated 8.8 years ago by ★ 1.1k • written 8.8 years ago by ▴ 10
1
vote
14
replies
3.7k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 8.0 years ago by ▴ 870 • written 8.0 years ago by • 0
4
votes
5
replies
2.9k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina pvalue
updated 8.9 years ago by ▴ 830 • written 8.9 years ago by ▴ 260
2
votes
3
replies
2.5k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 7.1 years ago by 50k • written 7.1 years ago by • 0
0
votes
0
replies
2.4k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi illumina normalization beadarray
7.0 years ago hkarakurt ▴ 20
3
votes
6
replies
2.4k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma illumina microarray lmfit differential gene expression
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
0
votes
4
replies
2.4k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina annotation
updated 8.5 years ago by ★ 6.5k • written 8.5 years ago by ▴ 10
11
votes
5
replies
2.3k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat idat microarray illumina
updated 8.6 years ago by ▴ 400 • written 8.6 years ago by ▴ 30
2
votes
5
replies
2.3k
views
Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
limma lumi illumina gene expression data
updated 2.4 years ago by ▴ 10 • written 5.8 years ago by • 0
0
votes
6
replies
2.2k
views
Illumina bead array analysis
illumina beadarray
updated 14 months ago by ★ 1.1k • written 9.6 years ago by • 0
0
votes
3
replies
2.1k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 110
0
votes
1
reply
2.1k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 7.9 years ago by 50k • written 7.9 years ago by ▴ 30
1
vote
6
replies
2.1k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
8.5 years ago stuti.agrawal • 0
0
votes
7
replies
2.0k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 5.0 years ago by ★ 3.9k • written 5.0 years ago by • 0
0
votes
2
replies
1.9k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi minfidata illumina methylation dmpfinder
updated 9.6 years ago by 65k • written 9.6 years ago by • 0
1
vote
5
replies
1.9k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm illumina beadarraysnp
updated 9.2 years ago by ▴ 1000 • written 9.2 years ago by ▴ 30
0
votes
4
replies
1.9k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
updated 7.6 years ago by • 0 • written 7.7 years ago by • 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.1 years ago by 65k • written 6.1 years ago by • 0
0
votes
2
replies
1.9k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 7.0 years ago by ★ 3.9k • written 7.0 years ago by • 0
0
votes
2
replies
1.8k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray illumina methylation microarray
updated 8.6 years ago by 21k • written 8.6 years ago by • 0
1
vote
4
replies
1.8k
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 5.7 years ago by 65k • written 5.7 years ago by ▴ 30
0
votes
0
replies
1.7k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray beadarray Illumina Veracode
9.2 years ago lacion • 0
1
vote
1
reply
1.7k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 10
0
votes
7
replies
1.6k
views
getting error in processSwathData command from the beadarray package
microarray beadarray illumina
updated 9.1 years ago by ★ 6.5k • written 9.1 years ago by • 0
2
votes
4
replies
1.6k
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 3.3 years ago by 50k • written 3.4 years ago by • 0
7
votes
4
replies
1.6k
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 8.3 years ago by 65k • written 8.3 years ago by ▴ 20
0
votes
1
reply
1.6k
views
Error regarding installation and loading of "Lumi" Package
software error microarray illumina
updated 9.3 years ago by ★ 13k • written 9.3 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Annotation problems regarding quality information for Illumina HumanHT-12 v4-illuminaHumanv4.db
illumina human ht-12 v4 illuminahumanv4.db filtering on probe annotation illumina
updated 8.9 years ago by ★ 6.5k • written 8.9 years ago by ▴ 830
0
votes
3
replies
1.6k
views
MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
7.3 years ago annabelle.congras ▴ 10
2
votes
3
replies
1.6k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 7.7 years ago by 50k • written 7.7 years ago by ▴ 40
0
votes
4
replies
1.6k
views
minfi sample limit
minfi illumina illimina 450k methylation methylation
updated 8.1 years ago by ★ 6.5k • written 8.1 years ago by ▴ 40
6
votes
9
replies
1.5k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma illumina microarray multifactorial design batch effect
updated 7.9 years ago by 50k • written 7.9 years ago by ▴ 80
0
votes
1
reply
1.5k
views
Error in Matrix
minfi methylation EPIC microarray illumina
updated 8.0 years ago by ★ 6.5k • written 8.0 years ago by • 0
1
vote
2
replies
1.5k
views
minfi package QC report error?
minfi methylation illumina
9.5 years ago Brian Smith ▴ 120
0
votes
3
replies
1.5k
views
How can I pre-process illumina raw file
illumina microarray
updated 6.7 years ago by 65k • written 6.7 years ago by ▴ 260
2
votes
1
reply
1.5k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 8.5 years ago by 50k • written 8.5 years ago by ▴ 80
0
votes
0
replies
1.5k
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads methylation illumina epic microarray
7.7 years ago rasii • 0
1
vote
3
replies
1.4k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
6.8 years ago ezrabekele17 • 0
2
votes
1
reply
1.4k
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
1
vote
1
reply
1.4k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
written 6.0 years ago by • 0
0
votes
0
replies
1.4k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina 450k ChAMP paired test
8.2 years ago walter_teng • 0
0
votes
0
replies
1.4k
views
minfi v1.14 through champ: read.450k error with file path name
minfi champ illumina 450k
8.7 years ago jeroen • 0
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 6.4 years ago by ▴ 120 • written 6.4 years ago by • 0
1
vote
2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 5.4 years ago by ★ 1.3k • written 5.4 years ago by • 0
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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