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Showing :
MicroarrayData
•
reset
6
votes
4
replies
1.2k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
3.1 years ago
snijesh
▴ 20
0
votes
2
replies
716
views
How to extract probe level intensity after rma() normalization
MicroarrayData
AffymetrixChip
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
Haoran
• 0
3
votes
5
replies
1.5k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 2.7 years ago by
Gordon Smyth
50k • written 2.8 years ago by
Emma
• 0
0
votes
1
reply
499
views
Finding negative control in the array using R
R
MicroarrayData
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
Fatemeh
• 0
2
votes
2
replies
888
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
19 months ago
Fatemeh
• 0
0
votes
2
replies
2.0k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
2.9 years ago
waiyin0923
• 0
0
votes
1
reply
574
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Aleksandra
• 0
5
votes
8
replies
1.3k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 3 months ago by
Shaimaa Gamal
• 0 • written 10 months ago by
pg45863
▴ 10
0
votes
2
replies
1.6k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
3.1 years ago
jpwl2
• 0
0
votes
3
replies
504
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData
hta20transcriptcluster.db
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
yaxade2481
• 0
3
votes
9
replies
1.4k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
3.1 years ago
Daniel.Schnell
• 0
1
vote
1
reply
1.1k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Caitlin
▴ 50
0
votes
2
replies
859
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
14 months ago
dqt
• 0
1
vote
1
reply
1.2k
views
How do I adjust for other factors in Limma differential expression analysis?
limma
Microarray
MicroarrayData
arrays
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
Emma
• 0
1
vote
1
reply
606
views
IS DGE possible with normalized microarray expression data and Limma ?
limma
MicroarrayData
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
waltheja
• 0
0
votes
4
replies
870
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
2.0 years ago • updated 24 months ago
Haoran
• 0
0
votes
2
replies
741
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
23 months ago
amir.rakhimov.b
• 0
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
RMP87
• 0
0
votes
8
replies
1.4k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
21 months ago
YC
• 0
0
votes
1
reply
832
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 2.3 years ago by
James W. MacDonald
65k • written 2.3 years ago by
biomyscience
• 0
4
votes
7
replies
321
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
0
votes
1
reply
663
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr
raw
Agilent
MicroarrayData
import
updated 2.4 years ago by
Gordon Smyth
50k • written 2.4 years ago by
irina.st.louis4
• 0
1
vote
2
replies
105
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
2 days ago
Mj.A.
• 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
22 months ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
777
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
22 months ago
Mikołaj Mierzejewski
• 0
0
votes
17
replies
2.1k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 14 months ago by
Gordon Smyth
50k • written 17 months ago by
Sam
• 0
0
votes
2
replies
618
views
Adj. P-value identical and high for all the genes
MicroarrayData
2.5 years ago
Adriana
• 0
0
votes
6
replies
324
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
21 days ago • updated 2 days ago
Lily Cheang
• 0
0
votes
1
reply
636
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Sam
• 0
2
votes
1
reply
488
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData
Annotation
GEOdata
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Michele Claire
• 0
2
votes
2
replies
516
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
17 months ago
evan.j.williams
▴ 10
1
vote
2
replies
686
views
Error in getCdfInfo(object) :
MicroarrayData
11 months ago
kobra
• 0
0
votes
0
replies
575
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
13 months ago
jsharif
• 0
0
votes
0
replies
477
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
19 months ago
Fatemeh
• 0
34 results • Page
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May be documented by the software you are using? https://github.com/lpantano/DEGreport
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
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mercedeh.movassagh
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Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
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