Showing : microarray • reset
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 8 weeks ago by 53k • written 16.6 years ago by ▴ 10
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2
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559
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affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 5 months ago by 68k • written 5 months ago by • 0
0
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1
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409
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
1
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8
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2.3k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 months ago by • 0
1
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5
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2.7k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.6 years ago by ▴ 10
1
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4
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5.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.8 years ago by • 0
2
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2
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4.0k
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Biostatistician Position: UMass Medical School
Microarray Microarray
written 18.2 years ago by ▴ 190
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2
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1.3k
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.4 years ago by ▴ 70
1
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2
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1.6k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.4 years ago Abdul ▴ 20
2
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2
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1.1k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.4 years ago Abdul ▴ 20
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2
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1.2k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
1
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6
replies
2.9k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.1 years ago by 53k • written 5.0 years ago by ▴ 20
2
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2
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1.2k
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
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0
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1.0k
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.5 years ago agamemnon • 0
0
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1
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1.1k
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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2
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1.6k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.7 years ago dqt • 0
0
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2
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1.1k
views
Celfiles not reading in
Microarray
written 2.7 years ago by • 0
3
votes
2
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8.6k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 2.8 years ago by ▴ 200 • written 7.8 years ago by • 0
6
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6
replies
2.1k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
2.8 years ago Sara ▴ 20
0
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17
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4.0k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.6 years ago by 53k • written 2.9 years ago by • 0
0
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1
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1.1k
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
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8
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2.1k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
3.2 years ago YC • 0
2
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13
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5.6k
views
Error in using r
microarray
updated 3.3 years ago by • 0 • written 8.9 years ago by • 0
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4
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1.5k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
3.3 years ago S • 0
1
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2
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1.3k
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
3.3 years ago Mikołaj Mierzejewski • 0
1
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2
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1.8k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
3.3 years ago Mikołaj Mierzejewski • 0
4
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10
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2.8k
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
3.3 years ago Yang Shi ▴ 10
3
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4
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2.6k
views
Quantile Normalization after rma or not?
limma Microarray oligo
3.3 years ago Yang Shi ▴ 10
2
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2
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1.2k
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
3.3 years ago Yang Shi ▴ 10
2
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5
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3.6k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.3 years ago nhaus ▴ 70
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2
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1.2k
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
3.4 years ago amir.rakhimov.b • 0
1
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2
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2.2k
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Time course experiment using limma
limma Multi-levelExperiments Microarray
3.4 years ago Wendy ▴ 10
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12
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2.3k
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Annotating featureData to an affymetrix Xcel microarray
Microarray
3.4 years ago Adam • 0
0
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0
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982
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
3.5 years ago emily • 0
1
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7
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10.0k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.5 years ago by • 0 • written 6.6 years ago by ▴ 10
2
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5
replies
2.6k
views
Adjust for base line gene expression in limma model
limma Microarray
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
4
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6
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1.9k
views
RMA on different disease labels
rma background microarray normalization
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
1
vote
1
reply
1.7k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 50
5
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2
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3.4k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 3.0 years ago by 53k • written 4.1 years ago by ▴ 10
0
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1
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1.6k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 4.1 years ago by ▴ 90 • written 4.2 years ago by ▴ 10
3
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5
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2.3k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 4.2 years ago by 53k • written 4.3 years ago by • 0
1
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1
reply
2.1k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
1
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2
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2.1k
views
RUV4 for microarrays
RUV4 RUV Microarray
4.4 years ago Antonio • 0
0
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2
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2.6k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
4.4 years ago waiyin0923 • 0
0
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1
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1.2k
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 4.4 years ago by ★ 4.1k • written 4.4 years ago by • 0
1
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2
replies
2.1k
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
4.5 years ago • updated 4.4 years ago a.deb • 0
3
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3
replies
1.8k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4.5 years ago FedeXandeR • 0
0
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2
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2.3k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.6 years ago jpwl2 • 0
9
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4
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1.8k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.6 years ago snijesh ▴ 200
1
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2
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1.9k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.6 years ago Dan ▴ 20
2,319 results • Page 1 of 47
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Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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