Showing : Microarray • reset
32
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0
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38k
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limma moderated t-statistics and B-statistics
Microarray limma
19.6 years ago • updated 3.5 years ago Gordon Smyth 50k
2
votes
5
replies
30k
views
Row labels in a heatmap
Microarray Microarray
updated 11.8 years ago by 65k • written 11.8 years ago by ▴ 60
0
votes
2
replies
22k
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Installing EnhancedVolcano package in R
microarray software error
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by • 0
0
votes
0
replies
17k
views
1000 R tutorials/Links
Sequencing Microarray Genetics Visualization Network Bayesian Classification Clustering
13.9 years ago David Lyon ▴ 340
0
votes
10
replies
17k
views
Fine tuning heatmap.2 graphics
Microarray Microarray
updated 18.1 years ago by ▴ 290 • written 18.1 years ago by ▴ 70
0
votes
7
replies
15k
views
How to adjust the Heatmap.2 color key
Microarray GeneSpring Microarray GeneSpring
15.8 years ago Martin Bonke ▴ 40
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 10.2 years ago by 65k • written 10.2 years ago by ▴ 350
7
votes
1
reply
15k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 14 months ago by • 0 • written 10.0 years ago by ▴ 40
1
vote
12
replies
12k
views
Using limma for quantitative proteomics data
Microarray Proteomics limma Microarray Proteomics limma
11.8 years ago Yong Li ▴ 80
28
votes
8
replies
12k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 6.6 years ago by 50k • written 9.1 years ago by ▴ 150
0
votes
6
replies
11k
views
Package version of Bioconductor cannot be unloaded, Error in unloadNamespace(package),help!!
microarray software error hgu133plus2.db
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
5
votes
2
replies
11k
views
lowess vs. loess
Microarray Normalization
updated 7.9 years ago by 50k • written 20.6 years ago by ▴ 30
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.7 years ago by • 0 • written 13.5 years ago by ▴ 120
6
votes
1
reply
11k
views
How to combine multiple probes representing a single gene?
microarray affy eset
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 20
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
0
votes
2
replies
10.0k
views
problems with "cannot allocate vector of size.."
Microarray gcrma Microarray gcrma
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ▴ 70
0
votes
4
replies
8.9k
views
Agilent 2-color Microarray data analysis tutorial
Microarray Visualization Clustering Microarray Visualization Clustering
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 140
0
votes
0
replies
8.8k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
9.9 years ago Guest User ★ 13k
5
votes
7
replies
8.7k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 30
8
votes
15
replies
8.6k
views
Design matrix for continuous independent variable in limma
limma microarray
8.3 years ago Linda Chaba ▴ 10
0
votes
2
replies
8.0k
views
heatmap.2 function and the scale option
Microarray Clustering Microarray Clustering
updated 12.5 years ago by ▴ 80 • written 12.6 years ago by ▴ 560
12
votes
9
replies
7.9k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
9.1 years ago svlachavas ▴ 830
2
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2
replies
7.9k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 8.2 years ago by ▴ 760 • written 8.2 years ago by • 0
1
vote
7
replies
7.5k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 2.1 years ago by • 0 • written 5.2 years ago by ▴ 10
0
votes
3
replies
6.8k
views
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Microarray Normalization Microarray Normalization
updated 16.1 years ago by ★ 13k • written 16.1 years ago by ▴ 20
0
votes
4
replies
6.8k
views
Limma Volcano Plot Highlight Top Genes by Color
limma microarray volcanoplot color
updated 5.5 years ago by 50k • written 5.5 years ago by • 0
3
votes
2
replies
6.6k
views
error with accessing GEOquery data
Microarray Microarray
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 340
0
votes
7
replies
6.6k
views
Annotating HTA 2.0 genes
microarray
9.4 years ago statistuta • 0
0
votes
1
reply
6.5k
views
plotting 3d image of pca analysis
Microarray Microarray
updated 13.9 years ago by ▴ 430 • written 13.9 years ago by ▴ 40
9
votes
4
replies
6.2k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
7.0 years ago Anna ▴ 50
2
votes
4
replies
6.2k
views
T-test for microarray data
limma microarray t.test
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
1
vote
2
replies
6.1k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 16 months ago by ▴ 20 • written 6.4 years ago by • 0
2
votes
10
replies
6.1k
views
Probeset ID's to entrez for Clariom D Human Affy Array
microarray affy
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
0
votes
3
replies
5.8k
views
median normalization
Microarray Normalization Microarray Normalization
updated 12.6 years ago by 65k • written 12.6 years ago by ▴ 580
0
votes
18
replies
5.8k
views
WGCNA error in network construction ?
microarray rnaseq
7.1 years ago m.azhar ▴ 10
1
vote
2
replies
5.7k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
0
votes
3
replies
5.6k
views
limma design and contrast matrix for paired experiment
Microarray limma edgeR Microarray limma edgeR
11.3 years ago Gordon Smyth 50k
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma microarray block paired linear model
9.4 years ago • updated 9.3 years ago vas ▴ 40
0
votes
2
replies
5.3k
views
How to read bgx files in R
microarray annotation illumina
8.8 years ago kanacska ▴ 10
0
votes
2
replies
5.3k
views
microarray: dealing with multi probes for one gene
Microarray limma Microarray limma
updated 16.9 years ago by ★ 1.3k • written 16.9 years ago by ▴ 10
0
votes
12
replies
5.2k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
11.2 years ago James W. MacDonald 65k
0
votes
2
replies
5.2k
views
sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 10.6 years ago by 50k • written 10.6 years ago by ▴ 120
0
votes
2
replies
5.1k
views
Packages not getting installed
Microarray GO annotate Microarray GO annotate
updated 14.9 years ago by 65k • written 14.9 years ago by ▴ 90
7
votes
8
replies
5.0k
views
Model matrix for anova in limma
limma design matrix microarray limma
updated 8.2 years ago by ★ 13k • written 8.3 years ago by ▴ 60
6
votes
6
replies
5.0k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 50
9
votes
10
replies
4.9k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 9.2 years ago by 50k • written 9.3 years ago by ▴ 10
5
votes
11
replies
4.8k
views
Duplicate gene ID's returned from limma microarray analysis
limma microarray
updated 24 months ago by 50k • written 7.3 years ago by ▴ 70
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 8.1 years ago by 50k • written 8.1 years ago by ▴ 80
6
votes
10
replies
4.7k
views
defining a function for multiple paired t.test in many rows of a microarray dataset
microarray r t.test bioconductor
updated 9.2 years ago by 50k • written 9.2 years ago by ▴ 830
0
votes
7
replies
4.7k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 10.6 years ago by ▴ 470 • written 10.6 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
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A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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