User: kentfung

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kentfung0
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Posts by kentfung

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Variance unstable after fitting to linear model with limma-voom pipeline
... Sorry I know what is happening. It's normal if I choose `trend=TRUE` when fitting. ...
written 12 days ago by kentfung0
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Variance unstable after fitting to linear model with limma-voom pipeline
... So I was doing a differential expression analysis with RNA-Seq data using limma-voom pipeline. However, the fit for mean-variance is not like a flat line at 1 but a curve (top: plot after voom; bottom: plot after fitting to linear model). Is it normal? Can I still use the results? ![voom_plotSA][1] ...
limma voom written 13 days ago by kentfung0
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Comment: C: How an index is built for each gene set collections using buildCustomIdx() index
... Hi fgol, I had the same problem and I ended up making a ensembl to entrez id master table. I couldn't find a quick way around it. What I did was check all the duplicated entries and see if there is actually a correct solution (wrong input) or they are actually duplicated, in which case I will delet ...
written 6 weeks ago by kentfung0
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Comment: C: Design matrix with intercept for multiple cluster comparison
... Hope this thread can still find you James. I have just realised that there's one more questions I have. The size of the cluster Is not even, which means it will be like: ``` > cluster <- as.factor(rep(c("A","B","C","D"), c(3,4,5,3))) > cluster [1] A A A B B B B C C C C C D D D Levels: A B ...
written 6 weeks ago by kentfung0
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Comment: C: Design matrix with intercept for multiple blocks comparison
... Thanks for correcting the terminology. I know very little about bioinformatics or statistics as you can tell. So it will be like, carry on from the example: ``` > dat0 = as.matrix(raw_data$counts) # this is the actual count matrix > mod1 = design > mod0 = cbind(mod1[,1]) > set.seed(12 ...
written 7 weeks ago by kentfung0
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Design matrix with intercept for multiple cluster comparison
... I have posted a similar question before but it was poorly formulated so I'll try to make it better this time. I have 258 samples and they are all settled in 26 different clusters, with some clusters with only 1 sample and some with over 40. The clusters are mutually exclusive. I will illustrate it ...
limma sva written 7 weeks ago by kentfung0 • updated 7 weeks ago by centralmenu100
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Comment: C: Design matrix for cohort with samples outside "block"
... Sorry I have reformulated the questions so it makes more sense ...
written 8 weeks ago by kentfung0
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Comment: C: Design matrix for cohort with samples outside "block"
... Sorry I have reformulated the questions. It should make more sense now. ...
written 8 weeks ago by kentfung0
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Design matrix for cohort with samples outside "block"
... Hi, I am using limma-voom for a RNA-Seq differential expression analysis. So there are 260 samples from leukaemia patients and they fall into different clusters except for some 40 samples. So let's say I have clusters A to H, each contains 5 - 40 samples, and then 40 samples that don't fall into an ...
limma sva voom written 8 weeks ago by kentfung0
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Comment: C: Finding genes in a gene set detected by ROAST (or FRY) in limma
... Hi Gordon, Thank you for suggesting the use of camera. I am quite new to the field and saw a review saying that self-contained gene set analysis is more specific and sensitive, so I just followed without thinking much. I will have a look at the paper and vignette again. Thanks a lot for your help. ...
written 3 months ago by kentfung0

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