User: Peter

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Peter0
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Posts by Peter

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Uneven number of treatment/control libraries
... Assuming your question is "is it OK to have different number of control / treatment replicates", then the answer is yes, it is OK. Is the badly prepared control library the same as the one that plots with the treatments? Could you provide more detail, such as the technique used (RNA-seq?) or the R ...
written 12 months ago by Peter0
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Comment: C: How to filter tximport output for edgeR?
... Using the guide then it would look like this: ... y <- DGEList(cts) keep <- rowSums(cpm(y) > 2) >= 3 y <- y[keep, , keep.lib.sizes=FALSE] But then I guess I need to recalculate the normalization factors, and also was not sure about the offset calculation. y$offset <- t(t(log(n ...
written 13 months ago by Peter0
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How to filter tximport output for edgeR?
... The tximport vignette describes the following steps for using the data with edgeR: https://github.com/mikelove/tximport/blob/master/vignettes/tximport.md library(edgeR) cts <- txi$counts normMat <- txi$length normMat <- normMat/exp(rowMeans(log(normMat))) library(edgeR) o <- log(calcN ...
edger rna-seq salmon tximport written 13 months ago by Peter0 • updated 13 months ago by Michael Love14k
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Comment: C: Trouble with Tximport
... I get the same error when using Gencode fasta files with salmon, because the quant.sf output becomes: Name Length EffectiveLength TPM NumReads ENST00000456328.2|ENSG00000223972.5|OTTHUMG00000000961.2|OTTHUMT00000362751.1|DDX11L1-002|DDX11L1|1657|processed_transcript| 1657 1456.57 ...
written 13 months ago by Peter0
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Comment: C: What is the correct contrast matrix if one treatment must be compared to both of
... Thank you for the comment, it's true that there are two rounds of error, although I think a more profound loss arises from not including the genes that are not DE against both controls. Also yes, there is the danger that the intersect approach ignores effects countering the placebo effect. However, ...
written 16 months ago by Peter0
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What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
... I have RNA-seq data from a 3-level 1-factorial experiment: non-treated control, placebo-treated negative control, and treated cells. I have 3 replicates for each. After running edgeR, and also looking at expression levels, I noticed that the negative control is not a good control, as it has DE gene ...
limma edger design matrix model.matrix contrast matrix written 16 months ago by Peter0 • updated 16 months ago by Gavin Kelly510

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