Showing : estimatedisp • reset
1
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3
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How estimateDisp, glmQLFit and glmQLFTest process my TMM normalized read count matrix?
edgeR glmQLFTest glmQLFit estimateDisp
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
9
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2
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1.9k
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Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
edger estimateDisp
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 30
1
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3
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5.7k
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edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1) (minimal working example included)
edgeR estimatedisp
8.7 years ago endrebak85 ▴ 40
3
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5
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2.7k
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Using Scran normalization with in edgeR
edger estimatedisp scran sizefactors
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 10
3
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10
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8.4k
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Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space in paired edgeR comparison
edger paired samples model.matrix estimatedisp
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 30
1
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2
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1.8k
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estimateDisp runs forever but not the trio estimateGLM
edger estimateDisp
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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