Showing : MicroarrayData • reset
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Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 5 weeks ago by ★ 4.7k • written 5 weeks ago by • 0
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
3 months ago Ai • 0
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2
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514
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Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
11 months ago Mj.A. • 0
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7
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DEG Filtering
MicroarrayData limma Genefiltering
updated 11 months ago by 52k • written 11 months ago by • 0
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6
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1.2k
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
12 months ago • updated 11 months ago Lily Cheang ▴ 10
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Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 18 months ago by 52k • written 18 months ago by • 0
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 14 months ago by • 0 • written 21 months ago by ▴ 10
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1.2k
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Error in getCdfInfo(object) :
MicroarrayData
22 months ago kobra • 0
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902
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.0 years ago agamemnon • 0
2
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1
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802
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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1.3k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.1 years ago dqt • 0
2
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2
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792
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
2.4 years ago evan.j.williams ▴ 10
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17
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3.3k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.1 years ago by 52k • written 2.4 years ago by • 0
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1
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743
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Finding negative control in the array using R
R MicroarrayData
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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696
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
2.5 years ago Fatemeh • 0
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2
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1.5k
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
2.6 years ago • updated 2.5 years ago Fatemeh • 0
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809
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
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970
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
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8
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1.9k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
2.7 years ago YC • 0
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2
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1.1k
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
2.7 years ago Mikołaj Mierzejewski • 0
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1.5k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
2.7 years ago Mikołaj Mierzejewski • 0
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1.0k
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
2.8 years ago amir.rakhimov.b • 0
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1.0k
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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4
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1.2k
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.9 years ago Haoran • 0
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1
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1.1k
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R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 3.2 years ago by 68k • written 3.3 years ago by • 0
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959
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Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr raw Agilent MicroarrayData import
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
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3
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1.5k
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Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
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2
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793
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Adj. P-value identical and high for all the genes
MicroarrayData
3.5 years ago Adriana • 0
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1.5k
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 50
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5
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2.2k
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Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 3.7 years ago by 52k • written 3.7 years ago by • 0
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1
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1.8k
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How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
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2
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.9 years ago waiyin0923 • 0
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2.0k
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WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.0 years ago jpwl2 • 0
8
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4
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1.6k
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.1 years ago snijesh ▴ 200
3
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9
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1.8k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4.1 years ago Daniel.Schnell • 0
36 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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