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DESeq countDataSets and arrayQualityMetrics (was: Re: DESeq estimateDispersion options for lower depth miRNA-seq)
Genetics Biobase arrayQualityMetrics DESeq Genetics Biobase arrayQualityMetrics DESeq
13.5 years ago Wolfgang Huber ★ 13k
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DESeq estimateDispersion options for lower depth miRNA-seq
Genetics arrayQualityMetrics DESeq Genetics arrayQualityMetrics DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 50
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DESeq estimateDispersion options for lower depth
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13.5 years ago Aggarwal, Praful ▴ 50
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Three tenure track assistant professorship openings at Inst. Behavioral Genetics, University of Colorado Boulder
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problems generating a gene2GOlist in topGO
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13.5 years ago Adaikalavan Ramasamy ▴ 100
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snpStats, read.long, alleles in two columns
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updated 13.5 years ago by ▴ 20 • written 13.5 years ago by ▴ 30
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Standard error and confidence intervals in DESeq?
Genetics DESeq Genetics DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 190
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13.6 years ago saikouy bah ▴ 30
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clippda: a package for clinical proteomics data analysis
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13.8 years ago Gordon Smyth 53k
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cause 'memory not mapped'
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14.3 years ago Pan Du ▴ 440
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updated 14.9 years ago by ★ 3.8k • written 14.9 years ago by ▴ 20
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downloading different kinds of microarray data
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Problems with arrayQualityMetrics
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337 results • Page 3 of 7
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure by James W. MacDonald 68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Answer: replace cat with message in glmTreat when lfc = 0 by Gordon Smyth 53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
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Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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