Showing : MicroarrayData • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
6 months ago Shaimaa Gamal • 0
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299
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Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
11 months ago Ai • 0
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2
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727
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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
19 months ago Mj.A. ▴ 20
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DEG Filtering
MicroarrayData limma Genefiltering
updated 19 months ago by 53k • written 19 months ago by • 0
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
19 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 2.2 years ago by 53k • written 2.2 years ago by • 0
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2.9k
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 22 months ago by • 0 • written 2.4 years ago by ▴ 10
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1.3k
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Error in getCdfInfo(object) :
MicroarrayData
2.5 years ago kobra • 0
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1.0k
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.7 years ago agamemnon • 0
2
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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1.7k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.8 years ago dqt • 0
2
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2
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1.0k
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
3.0 years ago evan.j.williams ▴ 10
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4.1k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.7 years ago by 53k • written 3.0 years ago by • 0
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827
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Finding negative control in the array using R
R MicroarrayData
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
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804
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
3.2 years ago Fatemeh • 0
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2
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1.8k
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
3.2 years ago Fatemeh • 0
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909
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
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1.1k
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
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2.2k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
3.3 years ago YC • 0
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1.3k
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
3.4 years ago Mikołaj Mierzejewski • 0
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1.8k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
3.4 years ago Mikołaj Mierzejewski • 0
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
3.5 years ago amir.rakhimov.b • 0
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1.2k
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
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4
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1.4k
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
3.6 years ago Haoran • 0
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1
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1.3k
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R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
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1
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1.1k
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Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr raw Agilent MicroarrayData import
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
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3
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1.7k
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Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
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2
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885
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Adj. P-value identical and high for all the genes
MicroarrayData
4.1 years ago Adriana • 0
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1.7k
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 50
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5
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2.4k
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Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 4.3 years ago by 53k • written 4.4 years ago by • 0
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1
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2.1k
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How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 4.4 years ago by ★ 4.0k • written 4.5 years ago by • 0
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2
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2.6k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
4.5 years ago waiyin0923 • 0
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2
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2.3k
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WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.7 years ago jpwl2 • 0
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4
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1.9k
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.7 years ago snijesh ▴ 200
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9
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2.2k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4.7 years ago Daniel.Schnell • 0
37 results • Page 1 of 1
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Answer: Issue with Soft-Thresholding in WGCNA by misty.chickadee.vckc • 0
Hi Maria, your detailed explanation is super helpful! The NA power estimate in WGCNA can be tricky. I've sometimes seen that when the data …
Comment: Interpretation of output of AffyRNAdeg and hist commands by debasainalsa • 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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