Showing : MicroarrayData • reset
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 19 months ago by 51k • written 23 months ago by • 0
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2
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2.3k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.4 years ago waiyin0923 • 0
5
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8
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1.9k
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 9 months ago by • 0 • written 16 months ago by ▴ 10
3
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5
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1.9k
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Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 3.2 years ago by 51k • written 3.3 years ago by • 0
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2
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1.8k
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WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
3.6 years ago jpwl2 • 0
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8
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1.7k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
2.2 years ago YC • 0
3
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9
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1.6k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.6 years ago Daniel.Schnell • 0
1
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1
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1.6k
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How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
8
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4
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1.5k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.6 years ago snijesh ▴ 200
1
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1
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1.4k
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.0 years ago by 67k • written 3.0 years ago by ▴ 50
1
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3
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1.3k
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Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
1
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2
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1.3k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
2.3 years ago Mikołaj Mierzejewski • 0
2
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2
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1.2k
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
2.1 years ago Fatemeh • 0
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2
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1.1k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
20 months ago dqt • 0
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4
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1.1k
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.5 years ago Haoran • 0
0
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1
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994
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
1
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2
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966
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Error in getCdfInfo(object) :
MicroarrayData
17 months ago kobra • 0
1
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2
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949
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
2.3 years ago Mikołaj Mierzejewski • 0
0
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2
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923
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
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2
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905
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
2.4 years ago amir.rakhimov.b • 0
2
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6
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887
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 months ago • updated 5 months ago Lily Cheang ▴ 10
0
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1
reply
830
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
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1
reply
815
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Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr raw Agilent MicroarrayData import
updated 2.9 years ago by 51k • written 2.9 years ago by • 0
5
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7
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797
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DEG Filtering
MicroarrayData limma Genefiltering
updated 5 months ago by 51k • written 6 months ago by • 0
0
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1
reply
790
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 19 months ago by 67k • written 19 months ago by • 0
0
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3
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785
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Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 13 months ago by 51k • written 13 months ago by • 0
0
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0
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771
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
19 months ago jsharif • 0
1
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1
reply
721
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
0
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2
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713
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Adj. P-value identical and high for all the genes
MicroarrayData
3.0 years ago Adriana • 0
2
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2
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678
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
23 months ago evan.j.williams ▴ 10
2
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1
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669
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 19 months ago by 67k • written 19 months ago by • 0
0
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1
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639
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Finding negative control in the array using R
R MicroarrayData
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
0
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0
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619
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
2.1 years ago Fatemeh • 0
1
vote
2
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358
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
5 months ago Mj.A. • 0
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Comment: Question on performing ANOVA-like analysis using limma by Gordon Smyth 51k
What does `sampleid` represent? If you use duplicateCorrelation(), then the blocking factor should be subject, it isn't clear from your que…
Answer: Question on performing ANOVA-like analysis using limma by Gordon Smyth 51k
In time course experiments such as this, it is essential to account for baseline variability between subjects, so the second analysis given…
Comment: AffylmGUI does not start wit R 4.4.1 by Gordon Smyth 51k
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Answer: rtracklayer accessing UCSC data table not working by James W. MacDonald 67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
Answer: For feline genome by James W. MacDonald 67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
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Comment: AffylmGUI does not start wit R 4.4.1
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
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