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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2.4k
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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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2.3k
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Biostatistician Position: UMass Medical School
Microarray Microarray
written 16.8 years ago by ▴ 190
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2
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669
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 11 months ago by ▴ 70
1
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2
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858
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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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640
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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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664
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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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635
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Question about avereps function of limma
avereps probes average limma Microarray
updated 13 months ago by 50k • written 13 months ago by ▴ 10
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0
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597
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
13 months ago jsharif • 0
0
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1
reply
611
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
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2
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896
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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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693
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Celfiles not reading in
Microarray
written 15 months ago by • 0
1
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2
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6.1k
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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
653
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 21 months ago by 50k • written 21 months ago by • 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
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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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801
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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
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
22 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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789
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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
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Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
23 months ago nhaus ▴ 30
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2
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761
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
23 months ago amir.rakhimov.b • 0
0
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2
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1.1k
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Time course experiment using limma
limma Multi-levelExperiments Microarray
2.0 years ago • updated 24 months ago Wendy • 0
0
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12
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1.5k
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Annotating featureData to an affymetrix Xcel microarray
Microarray
2.0 years ago Adam • 0
0
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0
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607
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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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7.5k
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Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 2.1 years ago by • 0 • written 5.2 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 2.3 years ago by • 0
4
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6
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1.2k
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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
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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
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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
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1.3k
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How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
1
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1.3k
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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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858
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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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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
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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
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2
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1.4k
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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
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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
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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 4.8 years ago by • 0
50 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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