User: b.curran

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b.curran0
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Posts by b.curran

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Comment: C: Matching columns to sample names
... Hi Leonardo - sorry for the delay in reply.  I've done as you suggested. There's something hinky somewhere though. I've been pulling out the gdc_file_id's from the metadata, and those file_id's aren't present when I search through the gdc data portal. The case id's that I pull from the metadata are ...
written 10 weeks ago by b.curran0
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Matching columns to sample names
... I'm examining the TCGA dataset from the recount2 website (https://jhubiostatistics.shinyapps.io/recount/). I've downloaded one of the Summarized experiments for the prostate cancer, and have managed to extract the counts using assay(). The column names of the dataframe extracted however, whilst they ...
recount written 11 weeks ago by b.curran0 • updated 11 weeks ago by Leonardo Collado Torres540
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BHC breaks on simple dataset
... So, I've had the BHC package working for a time course experiment before. I'm trying to use the multinomial option instead of the timecourse one and it's breaking, spectacularly. The basic use case in the documentation works, but is very easy to break.  I started off with matrix of data, 47 rows, 1 ...
bhc written 2.7 years ago by b.curran0 • updated 2.6 years ago by Rich Savage60
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Heatmaps in BHC package
... Quick, probably simple question that I can't find the answer to.    I'm using the BHC package. The paper associated with the package says that in addition to displaying the results as a dendrogram, it is possible to display the resulats as a heatmap using the package R heatmap command. It doesn't ...
bhc written 2.8 years ago by b.curran0 • updated 2.6 years ago by Rich Savage60
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Comment: C: data preparation for timecourse
... Primarily pathogen response genes. And I have been finding them with DESeq and EdgeR. The primary attraction of Timecourse was that I was thinking it would be good for finding genes D.E over the timecourse as a whole rather than all the pairwise comparisons I had done with DESeq. And the nifty expre ...
written 2.9 years ago by b.curran0
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Comment: C: data preparation for timecourse
... Apologies for the late reply.  Thank you for that though, that explains it quite clearly. In as much as that is a concept that I had grasped when reading the DESeq paper. I think some of the other links regarding heteroscedasticity somewhat confused me.  ...
written 2.9 years ago by b.curran0
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Comment: C: data preparation for timecourse
... I am indeed using DESeq2 for my analysis.  I have 57 samples of RNASeq data from two treatments spread over 10 time points (only got 3 replicates for control treatment at time zero :-/). When I run DeSeq2 pairwise, longitudinally along the inoculated samples, there is a bunch of interesting changes ...
written 3.0 years ago by b.curran0
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data preparation for timecourse
... I'm using the timecourse package in bioconductor. I have been obtaining size factors for each of the samples from DESeq's sizeFactors() before log transforming the raw data and using this in mb.long() from timecourse. Should I be doing this or is timecourse a package which handles the sample size n ...
timecourse written 3.0 years ago by b.curran0 • updated 3.0 years ago by Dario Strbenac1.4k
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Comment: C: Why does the order of data being input matter in Timecourse.R
... Thanks for the response. Also the catching of the error :) Sadly it wasn't that though. With the amended assay, I still get different results. Again, the first few genes are ranked the same and then it varies. And whilst the first few are the same, their hotellingT2 stat changes.  For size, for bo ...
written 3.0 years ago by b.curran0
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Why does the order of data being input matter in Timecourse.R
... So I'm not sure whether this is a bug or I'm missing something. I'm using timecourse to look at a bunch of genes over a period of 5 days. Section 2.2 of the timecourse manual tells me that I either have to assign time and replicate groups orn have my data ordered in a specific way that the package ...
timecourse written 3.0 years ago by b.curran0 • updated 3.0 years ago by James W. MacDonald45k

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