User: stan

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stan0
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South Africa/Pretoria
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Posts by stan

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Comment: C: How to get DESeq2 sizefactors from data imported using tximport
... Thanks again Michael, it's working fine now. ...
written 17 months ago by stan0
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Comment: C: How to get DESeq2 sizefactors from data imported using tximport
... Thanks a lot Michael,  I noticed normMatrix argument is not used for the estimateSizeFactorsForMatrix function, so instead would it make sense to calculate the geometric mean of each sample (column) from normalizationFactors(dds), and use that as the size factor for each sample?  Or should I just ...
written 17 months ago by stan0
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How to get DESeq2 sizefactors from data imported using tximport
... Hi, How can i get sizeFactors from sailfish output imported into DESeq2 using tximport. I got NULL after doing the following: > txi <- tximport(files, type="sailfish", tx2gene=tx2gene, dropInfReps=TRUE) > ddsTxi <- DESeqDataSetFromTximport(txi, colData = samples, design = ~ condition) ...
deseq2 sailfish tximport written 17 months ago by stan0 • updated 17 months ago by Michael Love20k
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Comment: C: ddCt calculation using bioconductor package
... Hi David, Where can I find ddCT version 1.24.0, because I have just installed ddCt from bioconductor but the version I am getting is 1.22.0 > packageVersion("ddCt") [1] ‘1.22.0’ I also have my qPCR data as .eds from QuantStudio 12k Flex and I very much want to analyze it using ddCT. So where ...
written 3.5 years ago by stan0
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Comment: C: [DESeq2] time series strain-specific differences over time
... Hi Michael, Just a quick question on the answer you gave for "Is there a way to take all time points into account? In order to find a gene that is DE in all time points between two groups?"  I followed your tutorial on the fission data for time series experiments, and i thought that taking a summa ...
written 3.6 years ago by stan0

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