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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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2
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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 GO Cancer Colon affy limma Microarray GO Cancer Colon affy limma
12.8 years ago James W. MacDonald 65k
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1.7k
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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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606
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help with matrix
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updated 14.2 years ago by 65k • written 14.2 years ago by ▴ 420
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873
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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
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14.9 years ago Dmitri Mouradov ▴ 20
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1.6k
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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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3
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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: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
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Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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