Showing : microarray • reset
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affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
10 hours ago akp9132 • 0
0
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1
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208
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 7 weeks ago by ★ 4.7k • written 7 weeks ago by • 0
1
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8
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1.6k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
1
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5
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2.5k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.1 years ago by ▴ 10
1
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4
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4.8k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.3 years ago by • 0
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2
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3.8k
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Biostatistician Position: UMass Medical School
Microarray Microarray
written 17.7 years ago by ▴ 190
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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 22 months ago by ▴ 70
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2
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1.4k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
23 months ago Abdul ▴ 20
2
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2
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983
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
23 months ago Abdul ▴ 20
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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 23 months ago by 52k • written 23 months ago by • 0
1
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6
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2.6k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 19 months ago by 52k • written 4.5 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 2.0 years ago by 52k • written 2.0 years ago by ▴ 10
0
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0
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911
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.1 years ago agamemnon • 0
0
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1
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923
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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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2
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1.4k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.2 years ago dqt • 0
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2
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970
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Celfiles not reading in
Microarray
written 2.2 years ago by • 0
3
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2
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8.0k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 2.3 years ago by ▴ 200 • written 7.3 years ago by • 0
6
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6
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1.8k
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
2.3 years ago Sara ▴ 20
0
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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
0
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1
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984
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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
0
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8
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1.9k
views
Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
2.7 years ago YC • 0
2
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13
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5.3k
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Error in using r
microarray
updated 2.8 years ago by • 0 • written 8.4 years ago by • 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
2.8 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
2.8 years ago Mikołaj Mierzejewski • 0
1
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2
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1.5k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
2.8 years ago Mikołaj Mierzejewski • 0
4
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10
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2.5k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
2.8 years ago Yang Shi ▴ 10
3
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4
replies
2.3k
views
Quantile Normalization after rma or not?
limma Microarray oligo
2.8 years ago Yang Shi ▴ 10
2
votes
2
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1.1k
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
2.8 years ago Yang Shi ▴ 10
2
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5
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3.1k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.9 years ago nhaus ▴ 70
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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
2.9 years ago amir.rakhimov.b • 0
1
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2
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1.9k
views
Time course experiment using limma
limma Multi-levelExperiments Microarray
2.9 years ago Wendy ▴ 10
0
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12
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2.1k
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Annotating featureData to an affymetrix Xcel microarray
Microarray
2.9 years ago Adam • 0
0
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0
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876
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
3.0 years ago emily • 0
1
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7
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9.3k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.0 years ago by • 0 • written 6.2 years ago by ▴ 10
2
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5
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2.3k
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Adjust for base line gene expression in limma model
limma Microarray
updated 3.2 years ago by 52k • written 3.2 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 3.4 years ago by 68k • written 3.4 years ago by • 0
1
vote
1
reply
1.6k
views
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
5
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2
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3.1k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 2.6 years ago by 52k • written 3.6 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 3.7 years ago by ▴ 80 • written 3.7 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 3.7 years ago by 52k • written 3.8 years ago by • 0
1
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1
reply
1.9k
views
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
1
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2
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1.9k
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RUV4 for microarrays
RUV4 RUV Microarray
3.9 years ago Antonio • 0
0
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2
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2.4k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.9 years ago waiyin0923 • 0
0
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1
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1.1k
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.9 years ago by ★ 4.1k • written 3.9 years ago by • 0
1
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2
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1.7k
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
4.0 years ago • updated 3.9 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
4.0 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
4.1 years ago jpwl2 • 0
8
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4
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1.6k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.1 years ago snijesh ▴ 200
1
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2
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1.7k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.1 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
4.1 years ago Daniel.Schnell • 0
50 results • Page 1 of 1
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
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Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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