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
23 days ago Mj.A. • 0
5
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7
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414
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DEG Filtering
MicroarrayData limma Genefiltering
updated 22 days ago by 50k • written 4 weeks ago by • 0
2
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6
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434
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 weeks ago • updated 24 days ago Lily Cheang ▴ 10
0
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3
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544
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Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 8 months ago by 50k • written 8 months ago by • 0
5
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8
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1.4k
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
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2
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729
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Error in getCdfInfo(object) :
MicroarrayData
12 months ago kobra • 0
0
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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
2
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1
reply
510
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 14 months ago by 65k • written 14 months ago by • 0
0
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1
reply
613
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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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897
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
15 months ago dqt • 0
2
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2
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544
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
18 months ago evan.j.williams ▴ 10
0
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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
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514
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Finding negative control in the array using R
R MicroarrayData
updated 19 months ago by 65k • written 19 months ago by • 0
0
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0
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491
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
20 months ago Fatemeh • 0
2
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2
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927
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
20 months ago Fatemeh • 0
1
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1
reply
621
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 21 months ago by 65k • written 21 months ago by • 0
0
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1
reply
654
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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
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
0
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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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736
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 23 months ago by 65k • written 23 months ago by • 0
0
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4
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894
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.1 years ago Haoran • 0
0
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1
reply
856
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 2.4 years ago by 65k • written 2.4 years ago by • 0
0
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1
reply
681
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr raw Agilent MicroarrayData import
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
1
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3
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1.1k
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Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
0
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2
replies
632
views
Adj. P-value identical and high for all the genes
MicroarrayData
2.6 years ago Adriana • 0
1
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1
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1.1k
views
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
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
reply
1.3k
views
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
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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2
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1.6k
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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
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
3
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9
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1.4k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.2 years ago Daniel.Schnell • 0
34 results • Page 1 of 1
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Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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