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Showing top results for tag: MicroArray • reset
0
votes
2
replies
381
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How to find potential batch effect for microarray samples?
Gene-expression Batch-effect Microarray
14 days ago by namck • 0
1
vote
3
replies
397
views
How can studies compare microarray datas with rna-seq?
RNA-seq microarray
updated 20 days ago by ★ 1.2k • written 25 days ago by ▴ 20
0
votes
1
reply
326
views
Need help to figure out what format this SNP calling data is.
SNP microarray
updated 4 weeks ago by 146k • written 4 weeks ago by • 0
1
vote
3
replies
444
views
Affymetrix microarray
gene-expression probes microarray
updated 5 weeks ago by 44k • written 6 weeks ago by ▴ 10
0
votes
1
reply
398
views
How to annoate the probe id to genes in Affymetrix Human Gene 2.0 ST Array [transcript (gene) version ?
biomart GEO microarray annotation
updated 8 weeks ago by ▴ 40 • written 8 weeks ago by ★ 4.3k
5
votes
6
replies
495
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Issue with converting Affy IDs to gene IDs/symbols
biomart affymetrix GEOquery microarray
updated 11 weeks ago by ▴ 430 • written 12 weeks ago by ▴ 420
7
votes
2
replies
412
views
Merged analysis of microarray datasets using R
R meta-analysis microarray
updated 12 weeks ago by ▴ 430 • written 3 months ago by ▴ 10
0
votes
2
replies
284
views
.tar files Microarray
Microarray
3 months ago by Bine ▴ 60
2
votes
3
replies
434
views
r script for wgcna analysis
microarray wgcna
updated 3 months ago by 3.7k • written 3 months ago by ▴ 10
0
votes
0
replies
183
views
How to pre-process raw microarray data?
limma microarray WGCNA
updated 3 months ago by 146k • written 3 months ago by ▴ 60
0
votes
0
replies
162
views
Creation of appropriate model matricies for Surrogate Variable Analysis (SVA)
normalization rna-seq sva microarray
3 months ago by qile0317 • 0
3
votes
2
replies
354
views
Combining microarray, RNA Seq, whole & exome sequencing
Microarray RNA
updated 4 months ago by 20k • written 4 months ago by ▴ 60
3
votes
2
replies
321
views
How to interpret this plotMDS of three disease clusters?
microarray plotMDS DEGs
updated 4 months ago by 84k • written 4 months ago by ▴ 60
0
votes
1
reply
349
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
updated 4 months ago by ★ 1.2k • written 4 months ago by ▴ 10
0
votes
0
replies
236
views
Combining Methylation Microarray data from different platforms
Microarray DNA EPIC 450K Methylation
5 months ago by James ▴ 30
1
vote
4
replies
661
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray Limma Agilent
5 months ago by hagl ▴ 20
0
votes
0
replies
223
views
Filter low express genes in microarray data
microarray
5 months ago by Chris ▴ 340
1
vote
1
reply
410
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray HumanHT-12v4 Illumina
updated 5 months ago by ★ 7.4k • written 5 months ago by • 0
0
votes
0
replies
281
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 5 months ago by 44k • written 5 months ago by • 0
0
votes
1
reply
390
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 5 months ago by 146k • written 5 months ago by ▴ 10
3
votes
1
reply
734
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 5 months ago by ▴ 20 • written 2.0 years ago by ★ 4.3k
1
vote
2
replies
351
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis R microarray DExMA combinedP
5 months ago by hagl ▴ 20
89
votes
24
replies
26k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 5 months ago by • 0 • written 4.0 years ago by 3.2k
0
votes
0
replies
209
views
NA values showing at duplicacy removal step
Microarray RNA-Seq
5 months ago by prithvi.mastermind ▴ 50
0
votes
0
replies
185
views
RobustRankAggreg rankMatrix subscript out of boundaries
RobustRankAggreg microarray R rankMatrix
6 months ago by hagl ▴ 20
0
votes
0
replies
204
views
meta-analysis on RNA seq AND microarray results
microarray RNA
6 months ago by liuyibin2005 • 0
2
votes
3
replies
437
views
Microarray pbrobe ID to gene ID problem
microarray
updated 6 months ago by 146k • written 6 months ago by • 0
0
votes
0
replies
273
views
How can I conduct a meta-analysis of RNA-seq or microarray data?
R RNA-seq microarray meta-analysis
6 months ago by wyt1995 ▴ 40
0
votes
1
reply
393
views
How is it possible to differentiate CG or AT heterozygous in Illumina Infinium Genotype Microarrays?
Heterozygous Genotype Microarray Infinium Illumina
updated 6 months ago by 4.3k • written 6 months ago by • 0
0
votes
0
replies
244
views
How can we deal with converted probe id in microarray?
R microarray probe ensembl
updated 6 months ago by 44k • written 6 months ago by ▴ 40
0
votes
6
replies
813
views
How can I see probe IDs in a microarray?
R microarray probe Affymetrix
7 months ago by wyt1995 ▴ 40
1
vote
7
replies
957
views
limma eBayes error in analysis of Illumina HumanHT-12 V4.0 expression beadchip data
R beadchip limma microarray Illumina
updated 7 months ago by ★ 1.2k • written 7 months ago by ▴ 20
1
vote
0
replies
326
views
Deconvolution: bulk and cell signature data from different platforms or technologies
CIBERSORT RNASeq Microarray deconvolution signature
7 months ago by zhang.jianhai ▴ 30
0
votes
1
reply
313
views
EnhancedVolcanop plot using GSE data
microarray GSE EnhancedVolcano
updated 8 months ago by ★ 3.0k • written 8 months ago by • 0
2
votes
5
replies
863
views
How to find genomic locations of SNP probes in EPIC chips
microarray snp epic
8 months ago by Bosberg ▴ 50
0
votes
0
replies
200
views
Error in intraspotCorrelation function (limma package): Max iterations exceeded??
microarray two-color limma intraspotCorrelation
updated 8 months ago by 146k • written 8 months ago by • 0
1
vote
1
reply
380
views
Gene expression of microarray data
Microarray
updated 8 months ago by ★ 7.4k • written 8 months ago by ▴ 120
2
votes
2
replies
590
views
Microarray analysis using Limma
microarray voom limma
8 months ago by mrashad ▴ 80
1
vote
2
replies
744
views
filtering low expressed gene in microarray for WGCNA
microarray WGCNA DESeq2
updated 8 months ago by 44k • written 9 months ago by ▴ 10
0
votes
0
replies
383
views
microarray data analysis in R
microarray
updated 9 months ago by 44k • written 9 months ago by • 0
0
votes
1
reply
395
views
Need Help Mapping Probe IDs to Gene Symbols
microarray
updated 9 months ago by ★ 1.8k • written 9 months ago by • 0
3
votes
1
reply
522
views
GEO dataset Microarray data analysis help
R microarray NCBI GEO
updated 10 months ago by 44k • written 10 months ago by ▴ 30
0
votes
3
replies
512
views
Microarray batch correction method suggestions
microarray batch-correction
updated 10 months ago by 44k • written 10 months ago by • 0
0
votes
1
reply
486
views
using RMA normalized microarray in Limma
GEOdatabase Microarray limma RMA
updated 10 months ago by 84k • written 10 months ago by ▴ 10
8
votes
6
replies
870
views
Microarray data analysis with and without contrast
microarray limma
10 months ago by 1769mkc ★ 1.2k
3
votes
9
replies
2.8k
views
Differential Expression Analysis using Bioconductor (RStudio) and GEO2R (GEO)
R gene DEG Bioconductor microarray
updated 11 months ago by • 0 • written 4.6 years ago by ▴ 30
0
votes
0
replies
375
views
Do different microarray chips yield different accuracy of polygenic scores?
microarray genome SNP polygenic-risk-score
updated 11 months ago by 44k • written 11 months ago by • 0
2
votes
2
replies
583
views
Analysis and results microarray data for research
microarray
updated 11 months ago by 146k • written 11 months ago by • 0
0
votes
0
replies
334
views
How to find OS duration, status information of patients in GSE1159 or GSE6891 (Microarray data analysis)
Microarray
11 months ago by sf.jeong510 ▴ 10
0
votes
4
replies
1.1k
views
Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
RNAseq DEseq time-course microarray
11 months ago by Shero ▴ 10
50 results • Page 1 of 1
Recent Votes
Answer: featureCounts segmentation fault
Answer: featureCounts segmentation fault
Comment: Cloud storage option for uploading Bioconductor Annotation package
Comment: Pedigree information
Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
A: What is the difference between GRCh37 and hs37? And hg19?
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Recent Replies
Comment: HTseq count issue, not aligning to features by GenoMax 146k
From original post > I have downloaded these from the same source So it would be unlikely.
Answer: HTseq count issue, not aligning to features by MolGeek ▴ 80
Have you checked if the cromosome names are represented the same way in both bam files and the gtf/gff? For example if in bams the chromoso…
Comment: Cloud storage option for uploading Bioconductor Annotation package by KABILAN ▴ 80
Okay.. for getting quick response I posted in both platforms...
Comment: featureCounts segmentation fault by Darked89 4.7k
`featureCounts` will also accept bgzip-ed and tabix indexed `GTF`. It may be a bit faster than using plain `GTF` but frankly I have not don…
Answer: Sankey + dot plot by dthorbur ★ 2.4k
Here is a rough outline you can start to play with using the dataset you provided. It creates separate Sankey and dot plots, but you can cr…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an by Ian 6.1k
Thank you I did not realise I could do that.
Comment: RNA-Seq mutation calling without germline data by Shred ★ 1.5k
Sorry for the delay. These are (legit, not stupid!) questions related to the usage, so would be better to do not flood the answer section o…
Comment: How to convert CSV format to VCF using Python? by Darked89 4.7k
You do not have enough columns to transform your `CSV` into `VCF` ver 4.2. There are just `CHROM POS ID REF ALT` end even that is being gen…
Comment: Cloud storage option for uploading Bioconductor Annotation package by GenoMax 146k
> I contacted hubs@bioconductor.org three days ago regarding SAS tokens. Perhaps you just need to be patient. Looks like you already post…
Comment: featureCounts segmentation fault by ATpoint 84k
Please show relevant code. This is almost certainly some issue with the GTF.
Comment: Are tens of DEGs still biologically meaningful? by DGTool ▴ 250
Personally, I feel this would not only depend on the experiment (which would be a large factor), but also what sort of thresholds and filte…
Answer: When to use integration with scRNASeq by ATpoint 84k
I want to stress here (as I did in many posts before) that methods like harmony do a per-cell batch correction. This means the method aims …
Comment: DESEQ with time series data on mutant vs. wild-type? by ATpoint 84k
Yes, this interaction term would capture genes where the difference between day and night is altered as a consequence of genotype. Note tho…
Comment: featureCounts segmentation fault by DGTool ▴ 250
Can you try running each part/command manually on the command line (instead of the bash script) to see if there might be an error/warning t…
Answer: LOC gene on opposite DNA-strand causes lower log2FC value? by ATpoint 84k
Find out if your library protocol is stranded or not. If standed then these two genes should be independent. If not stranded then they shou…
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