User: Amusement Pork

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Posts by Amusement Pork

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What does noise look like in the case of de novo transcriptome assembly?
... I've been involved with a RNA-Seq study of a non-model organism, and I have some lingering questions.    The study focused on chemotype differentiation in a non-model plant species. There's six distinct chemotypes/groups, and for each group the lab sampled three species. De novo assembly arrived at ...
assembly next-gen rna-seq written 4.9 years ago by Amusement Pork60 • updated 4.9 years ago by Biostar ♦♦ 20
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Comment: C: Limma calls all genes as differentially expressed - what am I doing wrong?
... Thanks bud, you were exactly right :)  ...
written 5.2 years ago by Amusement Pork60
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Comment: C: Limma calls all genes as differentially expressed - what am I doing wrong?
... Thank you so much! This community is terrific. To those that stumble on this answer by googling, here's how I generated the contrast matrix for 6 groups instead of two (my groups are A, C, G, L ,T, U): columnContrasts <- combn(levels(labels), 2) strContrasts <- apply(columnContrasts, 2, pas ...
written 5.2 years ago by Amusement Pork60
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Limma calls all genes as differentially expressed - what am I doing wrong?
... I have a design of 6 conditions with three replicates each, with expression levels for ~51000 transcription products. I'm using Limma's voom transformation to make my data approximately Gaussian, which by ocular pat-down seems to be the case:  The mean-variance estimation is visible here - kinda ...
differential-expression limma rna-seq voom written 5.2 years ago by Amusement Pork60 • updated 5.2 years ago by Manvendra Singh2.1k
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Comment: C: What's the real difference between these two types of methods for assessing diff
... Great answer, thank you.  As I understand you, there are two pointst: 1) The LASSO estimator is not consistent, and 2) The genes/features are not i.i.d., so even if it was consistent it would not yield a biologically meaningful answer.  In regards to 1), it was shown in 2008 that bootstrapping lea ...
written 5.2 years ago by Amusement Pork60
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Comment: C: What's the real difference between these two types of methods for assessing diff
... Good question: intuitively, if the conditions have no separating hyperplane then the resulting classifier will have the same performance as random guessing. You can test this by drawing the Area Under the Curve of the Receiver Operating Characteristic; in the case of random guessing, the AUC is a st ...
written 5.2 years ago by Amusement Pork60
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What's the real difference between these two types of methods for assessing differential expression?
... There's now tons of different packages available to do statistical analysis of gene expression data to assess differential expression. Many of them, like mainstays such as edgeR and DESeq, carefully estimate variance parameters for individual genes/contigs (through various fancy means), then fit lin ...
differential-expression methods rna-seq written 5.2 years ago by Amusement Pork60
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Comment: C: How does one construct the RNASeq expression (count) matrix in general?
... Hey Devon, this is literally what my data looks like, I have no access to the actual assembly.  ...
written 5.2 years ago by Amusement Pork60
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How does one construct the RNASeq expression (count) matrix in general?
... I have RNASeq data from a de novo transcriptome assembly. The data is not given to me in SAM/BAM files, but instead in some kind of proprietary format where each contig is represented nucleotide by nucleotide, and for each nucleotide you are given the number of hits for this nucleotide over the samp ...
rna-seq written 5.2 years ago by Amusement Pork60 • updated 5.2 years ago by Devon Ryan93k

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