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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
3.2 years ago
snijesh
▴ 20
5
votes
7
replies
404
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 21 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
5
votes
8
replies
1.4k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 4 months ago by
Shaimaa Gamal
• 0 • written 11 months ago by
pg45863
▴ 10
3
votes
9
replies
1.4k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
3.2 years ago
Daniel.Schnell
• 0
3
votes
5
replies
1.6k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 2.8 years ago by
Gordon Smyth
50k • written 2.9 years ago by
Emma
• 0
2
votes
2
replies
544
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
18 months ago
evan.j.williams
▴ 10
2
votes
6
replies
422
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
6 weeks ago • updated 23 days ago
Lily Cheang
▴ 10
2
votes
2
replies
922
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
20 months ago
Fatemeh
• 0
2
votes
1
reply
509
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData
Annotation
GEOdata
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Michele Claire
• 0
1
vote
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
Kevin Blighe
★ 3.9k • written 2.9 years ago by
Emma
• 0
1
vote
1
reply
619
views
IS DGE possible with normalized microarray expression data and Limma ?
limma
MicroarrayData
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
waltheja
• 0
1
vote
2
replies
727
views
Error in getCdfInfo(object) :
MicroarrayData
12 months ago
kobra
• 0
1
vote
2
replies
207
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
22 days ago
Mj.A.
• 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 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Caitlin
▴ 50
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
801
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
22 months ago
Mikołaj Mierzejewski
• 0
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
RMP87
• 0
0
votes
17
replies
2.2k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 14 months ago by
Gordon Smyth
50k • written 18 months ago by
Sam
• 0
0
votes
2
replies
630
views
Adj. P-value identical and high for all the genes
MicroarrayData
2.6 years ago
Adriana
• 0
0
votes
1
reply
653
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
0
votes
3
replies
543
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData
hta20transcriptcluster.db
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
yaxade2481
• 0
0
votes
1
reply
514
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
0
votes
2
replies
1.6k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
3.2 years ago
jpwl2
• 0
0
votes
2
replies
2.0k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
3.0 years ago
waiyin0923
• 0
0
votes
1
reply
609
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
0
votes
2
replies
735
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
0
votes
2
replies
896
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
15 months ago
dqt
• 0
0
votes
0
replies
489
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
20 months ago
Fatemeh
• 0
0
votes
4
replies
894
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
2.1 years ago
Haoran
• 0
0
votes
2
replies
761
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
23 months ago
amir.rakhimov.b
• 0
0
votes
8
replies
1.4k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
22 months ago
YC
• 0
0
votes
1
reply
854
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 2.4 years ago by
James W. MacDonald
65k • written 2.4 years ago by
biomyscience
• 0
0
votes
0
replies
596
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
13 months ago
jsharif
• 0
0
votes
1
reply
678
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr
raw
Agilent
MicroarrayData
import
updated 2.5 years ago by
Gordon Smyth
50k • written 2.5 years ago by
irina.st.louis4
• 0
34 results • Page
1 of 1
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Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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