Showing : MicroarrayData • reset
1
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Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
11 weeks ago Mj.A. • 0
5
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7
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541
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DEG Filtering
MicroarrayData limma Genefiltering
updated 11 weeks ago by 51k • written 3 months ago by • 0
2
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6
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649
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
3 months ago • updated 11 weeks ago Lily Cheang ▴ 10
0
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3
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649
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Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 10 months ago by 51k • written 10 months ago by • 0
5
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8
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1.6k
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 6 months ago by • 0 • written 12 months ago by ▴ 10
1
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2
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816
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Error in getCdfInfo(object) :
MicroarrayData
14 months ago kobra • 0
0
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0
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672
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
15 months ago jsharif • 0
2
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1
reply
567
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 16 months ago by 66k • written 16 months ago by • 0
0
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1
reply
675
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 16 months ago by 66k • written 16 months ago by • 0
0
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2
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986
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
17 months ago dqt • 0
2
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2
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589
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
20 months ago evan.j.williams ▴ 10
0
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17
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2.4k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 16 months ago by 51k • written 20 months ago by • 0
0
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1
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549
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Finding negative control in the array using R
R MicroarrayData
updated 21 months ago by 66k • written 21 months ago by • 0
0
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0
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552
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
22 months ago Fatemeh • 0
2
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2
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1.0k
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
22 months ago Fatemeh • 0
1
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1
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658
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 23 months ago by 66k • written 23 months ago by • 0
0
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1
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712
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 23 months ago by 51k • written 23 months ago by • 0
0
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8
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1.5k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
24 months ago • updated 23 months ago YC • 0
1
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2
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857
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
2.0 years ago Mikołaj Mierzejewski • 0
1
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2
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1.2k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
2.0 years ago Mikołaj Mierzejewski • 0
0
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2
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822
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
2.1 years ago amir.rakhimov.b • 0
0
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2
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811
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 2.1 years ago by 66k • written 2.1 years ago by • 0
0
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4
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953
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.2 years ago Haoran • 0
0
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1
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900
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 2.5 years ago by 66k • written 2.5 years ago by • 0
0
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1
reply
712
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr raw Agilent MicroarrayData import
updated 2.6 years ago by 51k • written 2.6 years ago by • 0
1
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3
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1.2k
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Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 2.7 years ago by 66k • written 2.7 years ago by • 0
0
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2
replies
665
views
Adj. P-value identical and high for all the genes
MicroarrayData
2.8 years ago Adriana • 0
1
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1
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1.2k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 2.8 years ago by 66k • written 2.8 years ago by ▴ 50
3
votes
5
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1.7k
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Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 3.0 years ago by 51k • written 3.0 years ago by • 0
1
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1
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1.4k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
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2
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2.1k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.2 years ago waiyin0923 • 0
0
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2
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1.7k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
3.3 years ago jpwl2 • 0
6
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4
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1.3k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.3 years ago snijesh ▴ 20
3
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9
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1.5k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.4 years ago • updated 3.3 years ago Daniel.Schnell • 0
34 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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