Showing : illumina • reset
0
votes
2
replies
196
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4 months ago sissialva21 • 0
2
votes
4
replies
261
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
3
replies
199
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
17 months ago erwin.tomasich ▴ 10
0
votes
7
replies
436
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Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 2.1 years ago by ★ 3.0k • written 2.1 years ago by • 0
1
vote
2
replies
516
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 2.5 years ago by ★ 1.2k • written 2.5 years ago by • 0
1
vote
4
replies
554
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 2.8 years ago by 57k • written 2.9 years ago by ▴ 20
0
votes
2
replies
518
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 3.0 years ago by 43k • written 3.0 years ago by • 0
2
votes
4
replies
461
views
The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
1
vote
1
reply
704
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 3.1 years ago by 57k • written 3.1 years ago by ▴ 10
1
vote
1
reply
572
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
updated 3.1 years ago by • 0 • written 3.1 years ago by • 0
1
vote
5
replies
501
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2 rna-seq illumina batch effect
updated 3.2 years ago by 33k • written 3.2 years ago by ▴ 40
0
votes
2
replies
412
views
BAM file into R from Illumina
bam file STAR Illumina
updated 3.2 years ago by ▴ 10 • written 3.2 years ago by • 0
0
votes
3
replies
829
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 3.2 years ago by 57k • written 3.2 years ago by • 0
1
vote
1
reply
560
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by • 0
0
votes
3
replies
948
views
How can I pre-process illumina raw file
illumina microarray
updated 3.9 years ago by 57k • written 3.9 years ago by ▴ 260
1
vote
3
replies
722
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
4.0 years ago ezrabekele17 • 0
0
votes
0
replies
476
views
minfi error with dmpfinder
methylation illumina
4.1 years ago indranipoddar • 0
0
votes
2
replies
896
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 4.1 years ago by ★ 3.0k • written 4.1 years ago by • 0
0
votes
0
replies
1.3k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi illumina normalization beadarray
4.1 years ago hkarakurt ▴ 20
2
votes
1
reply
825
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 4.3 years ago by 57k • written 4.3 years ago by • 0
2
votes
3
replies
1.5k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
3
replies
762
views
MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
4.5 years ago annabelle.congras ▴ 10
0
votes
1
reply
589
views
Problems in using lumi for importing illumina raw data
beadarray lumi normalization microarray illumina
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 90
0
votes
4
replies
945
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
updated 4.8 years ago by • 0 • written 4.9 years ago by • 0
0
votes
0
replies
760
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads methylation illumina epic microarray
4.8 years ago rasii • 0
2
votes
3
replies
912
views
lumiR [Illumina] error from non-normalized data
illumina
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 40
0
votes
0
replies
657
views
Illumina Genotyping in parallel raise an error
crlmm snp illumina
5.0 years ago nadne ▴ 10
6
votes
9
replies
827
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 5.0 years ago by 43k • written 5.0 years ago by ▴ 60
0
votes
1
reply
1.1k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 20
0
votes
2
replies
557
views
permutation with plink
illumina plink permutation
updated 5.1 years ago by 57k • written 5.1 years ago by • 0
0
votes
0
replies
516
views
Lumi Control Data
lumi illumina microarray
5.1 years ago m.a.bentley • 0
1
vote
14
replies
2.0k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 5.1 years ago by ▴ 800 • written 5.1 years ago by • 0
0
votes
1
reply
659
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 5.1 years ago by 57k • written 5.1 years ago by • 0
0
votes
1
reply
966
views
Error in Matrix
minfi methylation EPIC microarray illumina
updated 5.2 years ago by 6.5k • written 5.2 years ago by • 0
3
votes
15
replies
2.7k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
5.2 years ago rasii • 0
0
votes
4
replies
759
views
minfi sample limit
minfi illumina illimina 450k methylation methylation
updated 5.3 years ago by 6.5k • written 5.3 years ago by ▴ 40
0
votes
3
replies
1.1k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 110
0
votes
2
replies
787
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
5.3 years ago kritikamish99 ▴ 10
4
votes
8
replies
4.7k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
0
votes
0
replies
869
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina 450k ChAMP paired test
5.4 years ago walter_teng • 0
7
votes
4
replies
875
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 5.4 years ago by 57k • written 5.4 years ago by ▴ 20
0
votes
0
replies
795
views
Repetitive motifs on Illumina 450k derived sequences
illumina 450k motifs meme
5.4 years ago Gustavo Fernández Bayón ▴ 440
0
votes
0
replies
556
views
Problems using the savR package
savR illumina
5.5 years ago merella.stefania • 0
1
vote
1
reply
952
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 60
1
vote
6
replies
1.2k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
5.7 years ago stuti.agrawal • 0
1
vote
1
reply
731
views
Error genotyping with CRLMM
crlmm copynumber illumina
updated 5.7 years ago by ▴ 340 • written 5.7 years ago by • 0
0
votes
4
replies
1.5k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina annotation
updated 5.7 years ago by ★ 5.0k • written 5.7 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray illumina methylation microarray
updated 5.7 years ago by 21k • written 5.7 years ago by • 0
11
votes
5
replies
1.4k
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 5.8 years ago by ▴ 400 • written 5.8 years ago by ▴ 30
0
votes
0
replies
976
views
minfi v1.14 through champ: read.450k error with file path name
minfi champ illumina 450k
5.8 years ago jeroen • 0
50 results • Page 1 of 1
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Answer: Data input for aracne2regulon function in viper package by reef103 • 0
Hi @luna_p , I'm sorry I didn;t see this before. The error might be due to a lack of match between the genes in the network (regulators and…
Comment: deseq2 normalized data with heatmap by Kevin Blighe 3.1k
Hey Ian, specifically just for the heatmap and/or the clustering, we can additionally scale and center the `vsd` or `rld` data. The `scale…
Answer: Difference in mixed test for fry vs mroast by Gordon Smyth 43k
That's a fair question and you're right that the fry/mroast help page doesn't give currently enough information about the mixed p-values. …
Comment: deseq2 normalized data with heatmap by Ian • 0
Hey @kevin , Thanks for the helpful posts! I noticed in your link to this heatmap analysis, you used scale() and not vst(). However, in yo…
Comment: lmFit, continuous exposure, adjustment covariates by AyHi • 0
Dear Gordon, Thank you so much for your reply. It worked well! I just changed y to t because the protein values were included in dat in my…
Votes
Answer: How does the empirical Bayes moderation (eBayes) in the limma pipeline work?
Differential expression across gene features
C: DESeq on transcripts v/s genes
A: DESeq on transcripts v/s genes
DESeq on transcripts v/s genes
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