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ComBat
Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV
11.5 years ago SSc Array Core ▴ 10
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Some problems in combining ExpressionSet objects with the combine() function
Microarray Cancer Colon limma Microarray Cancer Colon limma
updated 12.8 years ago by 65k • written 12.8 years ago by ▴ 70
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help in 2-color data normalization
Normalization Cancer Colon Normalization Cancer Colon
updated 17.0 years ago by ▴ 50 • written 17.0 years ago by ▴ 890
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inSilicoMerging and Limma
Colon hgu133a2 hgu133plus2 limma inSilicoMerging Colon hgu133a2 hgu133plus2 limma
10.9 years ago Ed Siefker ▴ 230
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Package announcement: bsseq
Sequencing Alignment Cancer Colon bsseq Sequencing Alignment Cancer Colon bsseq
11.7 years ago Kasper Daniel Hansen ★ 6.5k
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contrasts.fit Error
Microarray Colon limma Microarray Colon limma
updated 19.6 years ago by 50k • written 19.6 years ago by ▴ 50
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Some problems in combining ExpressionSet objects with the combine() function
Microarray GO Cancer Colon affy limma Microarray GO Cancer Colon affy limma
12.8 years ago James W. MacDonald 65k
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Simple beadarraySNP analysis
SNP Normalization Cancer Colon PROcess beadarraySNP copynumber SNP Normalization Cancer
14.9 years ago Dmitri Mouradov ▴ 20
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What preprocessing needs to be done on the Experiment datasets
colon rstudio golubesets
updated 8.1 years ago by 65k • written 8.1 years ago by • 0
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Illumina 610 Quad SNP chips
SNP Cancer Colon SNP Cancer Colon
14.8 years ago Dmitri Mouradov ▴ 20
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help with matrix
Colon Colon
updated 14.2 years ago by 65k • written 14.2 years ago by ▴ 420
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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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