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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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inSilicoMerging and Limma
Colon hgu133a2 hgu133plus2 limma inSilicoMerging Colon hgu133a2 hgu133plus2 limma
10.9 years ago Ed Siefker ▴ 230
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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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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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Some problems in combining ExpressionSet objects with the combine() function
Microarray Cancer Colon limma Microarray Cancer Colon limma
updated 12.7 years ago by 65k • written 12.7 years ago by ▴ 70
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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
12.7 years ago James W. MacDonald 65k
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603
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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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Illumina 610 Quad SNP chips
SNP Cancer Colon SNP Cancer Colon
14.8 years ago Dmitri Mouradov ▴ 20
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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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help in 2-color data normalization
Normalization Cancer Colon Normalization Cancer Colon
updated 16.9 years ago by ▴ 50 • written 17.0 years ago by ▴ 890
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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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Comment: Error in champ.load(): The following specified files do not exist by Sherin • 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
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Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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