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Showing :
questions
4
votes
4
replies
1.1k
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
2.7 years ago
Konstantinos Yeles
▴ 80
4
votes
5
replies
2.0k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread
featurecounts
coercion
2.8 years ago • updated 2.7 years ago
Konstantinos Yeles
▴ 80
0
votes
0
replies
682
views
Regarding Genome versions
org.Hs.eg.db
BSgenome.Hsapiens.UCSC.hg38
3.2 years ago
Konstantinos Yeles
▴ 80
0
votes
2
replies
994
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb
ggbio
3.2 years ago
Konstantinos Yeles
▴ 80
4
votes
4
replies
1.5k
views
Issues loading a BAM file resulted from featurecounts
featurecount
rsubread
GenomicAlignments
4.0 years ago
Konstantinos Yeles
▴ 80
3
votes
12
replies
1.9k
views
Understanding group_by, reduce_ranges,
plyranges
granges
updated 4.4 years ago by
lee.s
▴ 70 • written 4.4 years ago by
Konstantinos Yeles
▴ 80
5
votes
6
replies
1.6k
views
Rsubread malloc(): memory corruption
Rsubread
malloc
align
updated 4.4 years ago by
Gordon Smyth
50k • written 4.6 years ago by
Konstantinos Yeles
▴ 80
6
votes
8
replies
2.7k
views
Ranges from a fasta file
biostrings
fasta
genomicranges
granges
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
Konstantinos Yeles
▴ 80
3
votes
5
replies
1.4k
views
Normalization for small non-coding RNA and multi-factor design
edger
limma voom
normalization
limma
updated 5.3 years ago by
James W. MacDonald
65k • written 5.3 years ago by
Konstantinos Yeles
▴ 80
6
votes
7
replies
1.8k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 5.3 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 5.3 years ago by
Konstantinos Yeles
▴ 80
7
votes
11
replies
4.7k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST
deseq2
boxplot
rnaseq
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
Konstantinos Yeles
▴ 80
1
vote
2
replies
1.1k
views
Correct construction of multiple design matrix with limma in an agilent microarray dataset
limma
multiple factor design
multiple time points
microarray
design and contrast matrix
updated 7.4 years ago by
James W. MacDonald
65k • written 7.4 years ago by
Konstantinos Yeles
▴ 80
3
votes
3
replies
2.1k
views
Explanation of an ANOVA approach of multiple coefficients in limma with topTable in a microarray analysis
limma
ANOVA
topTable
microarray
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
Konstantinos Yeles
▴ 80
2
votes
5
replies
2.5k
views
Question on how to proceed and analyze 9 microarray datasets of two different platforms to perform meta-analysis
microarray
meta-analysis
cross-platform normalization
statistical inference
updated 7.7 years ago by
alexvpickering
▴ 110 • written 8.2 years ago by
Konstantinos Yeles
▴ 80
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 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
Konstantinos Yeles
▴ 80
3
votes
6
replies
2.0k
views
Comparison of DE lists from different datasets of same microarray platform
microarray
DE-comparison
meta-analysis
scatter-plot
limma
8.0 years ago
Konstantinos Yeles
▴ 80
8
votes
10
replies
4.8k
views
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
limma
topTable
confidence interval
effect size
microarray
updated 8.0 years ago by
Gordon Smyth
50k • written 8.0 years ago by
Konstantinos Yeles
▴ 80
3
votes
12
replies
2.7k
views
Questions about complex design in limma regarding an agilent microarray dataset with multiple time points and different biological replicates
limma
design matrix
multiple time points
agilent microarrays
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Konstantinos Yeles
▴ 80
3
votes
3
replies
3.8k
views
Negative values after normalizing an agilent microarray dataset with limma
limma
agilent
offset
background correction
microarray
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
Konstantinos Yeles
▴ 80
3
votes
9
replies
2.4k
views
Annotation problem while quering hgug4112a.db with function select and duplicates for agilent microarray dataset
limma
annotation
agilent
hgug4112a
microarray
8.2 years ago
Konstantinos Yeles
▴ 80
2
votes
6
replies
2.7k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma
microarray
multifactorial design
duplicatecorrelation
model.matrix
8.3 years ago
Konstantinos Yeles
▴ 80
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 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
Konstantinos Yeles
▴ 80
2
votes
3
replies
1.2k
views
Problem with function combine regarding merging two data frames based on their common rows
bioconductor
merge data frames
combine
biocgenerics
8.4 years ago • updated 5 months ago
Konstantinos Yeles
▴ 80
2
votes
1
reply
3.9k
views
Find correct annotation for specific agilent platforms Whole Human Genome Microarray 4x44K
agilent
whole Human Genome Microarray 4X44K
annotationdbi
bioconductor
8.5 years ago
Konstantinos Yeles
▴ 80
24 results • Page
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