Showing : biologicalreplicates • reset
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Combining biological replicates from raw counts for use in differential gene expression/normalization (DESeq2 and edgeR)
differential gene expression biologicalreplicates raw_counts
updated 6.2 years ago by 67k • written 6.2 years ago by • 0
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7
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2.8k
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Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 7.0 years ago by ▴ 210 • written 7.7 years ago by • 0
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5
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3.9k
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DESeq2 - how to build design for multiple paired samples before/after with 2 conditions? (non-crossover)
deseq2 multifactorial design paired samples biologicalreplicates
7.8 years ago jahorst • 0
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1
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957
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Uneven number of treatment/control libraries
biologicalreplicates
8.1 years ago hac141 • 0
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6
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1.8k
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Effect of biological variation on tests
biologicalreplicates statistical test
updated 8.2 years ago by 51k • written 17.2 years ago by ▴ 320
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2
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1.3k
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seeking a paper or journal review about repeated multiple testing for Biological ChIP-seq replicates?
bioinformatics paper multiple treatments biologicalreplicates
updated 8.4 years ago by 51k • written 8.4 years ago by ▴ 80
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10
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DESEQ2 with 3 biological replicates for control and 1 biological replicate for treatment
DESEQ deseq2 deseq replicates biologicalreplicates
9.0 years ago wd ▴ 30
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Possible implementation of two class paired Rank Products in r with package RankProd
RankProd pairedtest bioconductor biologicalreplicates
9.6 years ago svlachavas ▴ 830
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Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Answer: HilBertVis install error by James W. MacDonald 67k
It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…
Votes
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
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