User: danielle.newby

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Posts by danielle.newby

<prev • 11 results • page 1 of 2 • next >
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Observation/case weighting in cluster analysis in R
... Hi everyone, I have a large matrix of over 100K observations to cluster using hierarchical clustering. Due to the large size, i do not have the computing power to calculate the distance matrix. To overcome this problem I chose to aggregate my matrix to merge those observations which were identical ...
clustering hclust hierarchical clustering weight written 4 months ago by danielle.newby0 • updated 4 months ago by Aaron Lun17k
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Up and down regulation in LIMMA for microarray dataset
... Hi, I need some clarification on my results as i have been getting myself very confused!  I have an an microarray experiment where i have controls and cases (dosed with a drug). I have used the following in the design matrix for limma:  design <- model.matrix( ~CLASS) ) This creates a design ...
microarray limma differential gene expression written 7 months ago by danielle.newby0 • updated 7 months ago by Aaron Lun17k
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... Hi Guido, Thanks for your comments really helpful! Yep i was using the RMA normalised data so now it works thank you! I have been told to do this plot even though its not really suitable for this type of chip - i dont think it will tell me anything different that i dont already know from my NUSE, R ...
written 7 months ago by danielle.newby0
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... Hi,  I am trying to follow this step and i am getting an error throwing up:  Error in vals[x, y] : subscript out of bounds  This is when i run the following line: > whatevs2 <- sapply(1:36, function(x) rowMeans(do.call(cbind, lapply(whatevs, function(y) log2(vals[y,x]))))) Is the exprs(d ...
written 7 months ago by danielle.newby0
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Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
... Hi, I was wondering if anyone knew where the python module is to carry out pathway analysis using the methods in the paper by Kim and Volsky (2005) in their paper "PAGE: Parametric Analysis of Gene Set Enrichment paper"? It is not clear if they produced a python module from the paper and if they di ...
microarray pathway analysis differential gene expression gsea page written 8 months ago by danielle.newby0 • updated 8 months ago by Guido Hooiveld2.2k
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Answer: A: LIMMA paired analysis adjusting for two continuous variables - microarray data
... Hi Everyone, Thank you so much for all your comments it is really helping with my learning of limma! I will try the ~ID + class and do abit more reading of the limma manual Thanks again, Danielle ...
written 8 months ago by danielle.newby0
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Comment: C: LIMMA paired analysis adjusting for two continuous variables - microarray data
... Hi Aaron, So i dont need to take into account using the correlation function that they are same people ? So you are saying that the above code is the same as the following: ID <- factor(rep(c(1,14,16,17,18), each=2)) class <- factor(rep(c("T0", "T2weeks"), 5)) design <- model.matrix( ...
written 8 months ago by danielle.newby0
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Comment: A: LIMMA paired analysis adjusting for two continuous variables - microarray data
... Hi Gavin, Thanks for your answer. I was originally using duplicate correlation to take into account subject correlation but the concern i have is that BMI and age will be the same regardless of being baseline or after 2weeks and that this is not the correct thing to do and i need some interaction ...
written 8 months ago by danielle.newby0
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LIMMA paired analysis adjusting for two continuous variables - microarray data
... Hi, I am analysing a dataset where i have subjects who were tested at baseline and then after 2 weeks of calorie restriction. I would like to see the genes DE between baseline and calorie restriction taking into account the persons age and BMI. As there is a before and after condition is only 2 wee ...
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Comment: C: Appropriate use of Limma Treat function
... Hi Aaron, Thank you so much for your reply it is very helpful. Just a bit more explanation of what i am doing. I have about 20 gene expression datasets and i want to see if the gene signatures extracted from these relate and/or can separate case versus control for another disease (bit of a long sh ...
written 8 months ago by danielle.newby0

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