Showing : microarray • reset
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pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
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4
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2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
2
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2
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2.4k
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Biostatistician Position: UMass Medical School
Microarray Microarray
written 16.8 years ago by ▴ 190
0
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2
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684
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
1
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2
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872
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
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2
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650
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
12 months ago Abdul ▴ 20
0
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2
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674
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 12 months ago by 50k • written 12 months ago by • 0
1
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6
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1.7k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 8 months ago by 50k • written 3.6 years ago by ▴ 20
2
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2
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644
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 13 months ago by 50k • written 13 months ago by ▴ 10
0
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0
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605
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
14 months ago jsharif • 0
0
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1
reply
622
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
0
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2
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908
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
15 months ago dqt • 0
0
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2
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702
views
Celfiles not reading in
Microarray
written 16 months ago by • 0
1
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2
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6.2k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 16 months ago by ▴ 20 • written 6.4 years ago by • 0
6
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6
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1.4k
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
17 months ago Sara ▴ 10
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17
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2.2k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 14 months ago by 50k • written 18 months ago by • 0
0
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1
reply
663
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 22 months ago by 50k • written 22 months ago by • 0
0
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8
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1.4k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
22 months ago YC • 0
2
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13
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4.5k
views
Error in using r
microarray
updated 22 months ago by • 0 • written 7.5 years ago by • 0
0
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4
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1.0k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
22 months ago S • 0
1
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2
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808
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
22 months ago Mikołaj Mierzejewski • 0
1
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2
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1.1k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
4
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10
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1.9k
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
23 months ago Yang Shi ▴ 10
3
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4
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1.6k
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Quantile Normalization after rma or not?
limma Microarray oligo
23 months ago Yang Shi ▴ 10
2
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2
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795
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Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
23 months ago Yang Shi ▴ 10
2
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5
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1.7k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
23 months ago nhaus ▴ 30
0
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2
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765
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
24 months ago amir.rakhimov.b • 0
0
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2
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1.1k
views
Time course experiment using limma
limma Multi-levelExperiments Microarray
2.0 years ago Wendy • 0
0
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12
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1.5k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.0 years ago Adam • 0
0
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0
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615
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
2.1 years ago emily • 0
1
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7
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7.6k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 2.1 years ago by • 0 • written 5.3 years ago by ▴ 10
2
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5
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1.8k
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Adjust for base line gene expression in limma model
limma Microarray
updated 2.3 years ago by 50k • written 2.4 years ago by • 0
4
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6
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1.2k
views
RMA on different disease labels
rma background microarray normalization
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
1
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1
reply
1.1k
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 2.6 years ago by 65k • written 2.6 years ago by ▴ 50
5
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2
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2.2k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 20 months ago by 50k • written 2.7 years ago by ▴ 10
0
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1
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1.1k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 2.8 years ago by ▴ 80 • written 2.8 years ago by ▴ 10
3
votes
5
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1.6k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 2.8 years ago by 50k • written 2.9 years ago by • 0
1
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1
reply
1.3k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
1
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2
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1.3k
views
RUV4 for microarrays
RUV4 RUV Microarray
3.0 years ago Antonio • 0
0
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2
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2.0k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.0 years ago waiyin0923 • 0
0
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1
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863
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Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
1
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2
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1.3k
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How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
3.1 years ago • updated 3.0 years ago a.deb • 0
3
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3
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1.3k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
3.1 years ago FedeXander • 0
0
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2
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1.6k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
3.2 years ago jpwl2 • 0
6
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4
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1.2k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
1
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2
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1.4k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
3.2 years ago Dan ▴ 20
3
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9
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1.4k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.2 years ago Daniel.Schnell • 0
0
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1
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1.3k
views
Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 3.2 years ago by 50k • written 15.4 years ago by ▴ 10
5
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8
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2.5k
views
how to annotate arrays
affy annotation microarray oligo
updated 3.4 years ago by 65k • written 8.7 years ago by • 0
0
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1
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1.1k
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 3.5 years ago by ★ 13k • written 4.9 years ago by • 0
50 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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