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insilicomerging
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table (pData(eset_NONE)[,"Study"]); table(pData(eset_NONE)[,"Disease"]);
affy
insilicomerging
6.0 years ago
pratikshasharma47
• 0
1
vote
3
replies
1.4k
views
Two microarrays merging (different experiments) - Error with esets (inSilicoMerging package)
inSilicoMerging
microarray
affymetrix microarrays
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
Adam_M
• 0
0
votes
1
reply
1.6k
views
InSilicoMerging error when using merge
insilicomerging
error
insilicodb
expressionset
8.2 years ago
andreas.pittroff
• 0
0
votes
3
replies
1.8k
views
error in drawing MDS plot for eset
MDSplot
geneexpression
insilicomerging
updated 9.1 years ago by
James W. MacDonald
68k • written 9.1 years ago by
Shamim Sarhadi
▴ 20
4
votes
8
replies
2.2k
views
Annotation Problem regarding double platform merged microarray eset using the inSilicoMerging R package, after differential expression analysis
inSilicoMerging
doubleannotation
affymetrix microarrays
limma
inSilicoDB
9.7 years ago
svlachavas
▴ 840
1
vote
2
replies
2.6k
views
Combining ExpressionSet objects : error with function merge() in "inSilicoMerging"
combine
expresiondataset
insilicomerging
9.8 years ago
alakatos
▴ 130
6
votes
4
replies
4.4k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging
batcheffect
limma
differential gene expression
bioconductor
updated 9.8 years ago by
Aaron Lun
★ 28k • written 9.8 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.1k
views
problem with insilicoMerging
insilicomerging
9.9 years ago
carol white
▴ 680
1
vote
5
replies
2.4k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma
bioconductor
batcheffect
Primeview
insilicomerging
updated 10.0 years ago by
Matthew McCall
▴ 830 • written 10.0 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.3k
views
'DWD' method in 'inSilicoMerging' packages
inSilicoMerging
10.4 years ago
Li Liu
▴ 100
0
votes
1
reply
1.5k
views
inSilicoMerging:::mergeCOMBAT covariates
inSilicoMerging
inSilicoMerging
updated 11.0 years ago by
Quentin De Clerck
▴ 10 • written 11.0 years ago by
François Lefebvre
▴ 50
0
votes
6
replies
2.7k
views
DWD method for batch effect removal
inSilicoMerging
inSilicoMerging
updated 11.7 years ago by
Dan Tenenbaum
★ 8.2k • written 11.7 years ago by
Li Liu
▴ 100
0
votes
2
replies
2.1k
views
inSilicoMerging and Limma
Colon
hgu133a2
hgu133plus2
limma
inSilicoMerging
Colon
hgu133a2
hgu133plus2
limma
11.9 years ago
Ed Siefker
▴ 230
13 results • Page
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Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2
by
cold.wolverine.arku
• 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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