Showing : microarray • reset
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428
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affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
0
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1
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264
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 3 months ago by ★ 4.8k • written 3 months ago by • 0
1
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8
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1.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
1
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5
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2.6k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.2 years ago by ▴ 10
1
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4
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5.1k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.4 years ago by • 0
2
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2
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3.9k
views
Biostatistician Position: UMass Medical School
Microarray Microarray
written 17.8 years ago by ▴ 190
0
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2
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1.1k
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 24 months ago by ▴ 70
1
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2
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1.5k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.0 years ago Abdul ▴ 20
2
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2
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1.0k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.0 years ago Abdul ▴ 20
0
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2
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1.1k
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
1
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6
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2.7k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 20 months ago by 52k • written 4.6 years ago by ▴ 20
2
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2
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1.1k
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 2.1 years ago by 52k • written 2.1 years ago by ▴ 10
0
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0
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932
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.2 years ago agamemnon • 0
0
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1
reply
950
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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2
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1.4k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.3 years ago dqt • 0
0
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2
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988
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Celfiles not reading in
Microarray
written 2.3 years ago by • 0
3
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2
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8.2k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 2.4 years ago by ▴ 200 • written 7.4 years ago by • 0
6
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6
replies
1.9k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
2.4 years ago Sara ▴ 20
0
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17
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3.6k
views
Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.2 years ago by 52k • written 2.5 years ago by • 0
0
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1
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1.0k
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
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8
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2.0k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
2.8 years ago YC • 0
2
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13
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5.4k
views
Error in using r
microarray
updated 2.9 years ago by • 0 • written 8.5 years ago by • 0
0
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4
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1.4k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
2.9 years ago S • 0
1
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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
2.9 years ago Mikołaj Mierzejewski • 0
1
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2
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1.6k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
2.9 years ago Mikołaj Mierzejewski • 0
4
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10
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2.6k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
2.9 years ago Yang Shi ▴ 10
3
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4
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2.4k
views
Quantile Normalization after rma or not?
limma Microarray oligo
2.9 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
2.9 years ago Yang Shi ▴ 10
2
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5
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3.3k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.0 years ago nhaus ▴ 70
0
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2
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1.1k
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
3.0 years ago amir.rakhimov.b • 0
1
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2.0k
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Time course experiment using limma
limma Multi-levelExperiments Microarray
3.0 years ago Wendy ▴ 10
0
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12
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2.1k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
3.0 years ago Adam • 0
0
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0
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897
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
3.1 years ago emily • 0
1
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7
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9.5k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.1 years ago by • 0 • written 6.3 years ago by ▴ 10
2
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5
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2.4k
views
Adjust for base line gene expression in limma model
limma Microarray
updated 3.3 years ago by 52k • written 3.4 years ago by • 0
4
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6
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1.7k
views
RMA on different disease labels
rma background microarray normalization
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
1
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1
reply
1.6k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 50
5
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2
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3.2k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 2.7 years ago by 52k • written 3.7 years ago by ▴ 10
0
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1
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1.5k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 3.8 years ago by ▴ 80 • written 3.8 years ago by ▴ 10
3
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5
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2.2k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 3.8 years ago by 52k • written 3.9 years ago by • 0
1
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1
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1.9k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
1
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2
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2.0k
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RUV4 for microarrays
RUV4 RUV Microarray
4.0 years ago Antonio • 0
0
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2
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2.5k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
4.0 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 4.0 years ago by ★ 4.1k • written 4.0 years ago by • 0
1
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2
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1.8k
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
4.1 years ago • updated 4.0 years ago a.deb • 0
3
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3
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1.7k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4.1 years ago FedeXandeR • 0
0
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2
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2.1k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.2 years ago jpwl2 • 0
9
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4
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1.7k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.2 years ago snijesh ▴ 200
1
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2
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1.8k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.2 years ago Dan ▴ 20
3
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9
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1.9k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4.2 years ago Daniel.Schnell • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind; Error: No sites have activity greater than filter value by etiennedanis • 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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