User: anupriya.dalmia

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Posts by anupriya.dalmia

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Comment: C: Design matrix for regressing gene expression on a continuous variable - age
... Yes, I plotted different clusters separately, of course :-) So I have lost the sample names (colnames) while running the analysis. To be able to plot these graphs, I would need the meta-information that correlates the sample name with their age. Is there a way to get this information back? I presu ...
written 15 months ago by anupriya.dalmia0
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Comment: C: Design matrix for regressing gene expression on a continuous variable - age
... Thanks again, Aaron. Okay so I was able to cluster the DE genes based on the fitted values and also plotted the logged values of the genes as line graphs against age but do not see any specific trends. Would it be better to plot the fitted values instead? Also, are there any other ways in which I c ...
written 15 months ago by anupriya.dalmia0
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Comment: C: Design matrix for regressing gene expression on a continuous variable - age
... Hi Aaron, Thanks again for your reply. >One approach to simplify interpretation would be to (i) find all DE genes using the spline model, (ii) cluster the genes based on their fitted values, and (iii) annotate the clusters, e.g., early responders, late responders, peaking genes. This will allow ...
written 15 months ago by anupriya.dalmia0
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Comment: C: Design matrix for regressing gene expression on a continuous variable - age
... Thanks for your reply, Aaron. So what I gather here is that the p-values from the spline model will help us interpret if there is any overall trend at all (without forcing linearity) but the logFC values from the simple model would determine whether that gene is, on the whole, going up/down with ag ...
written 16 months ago by anupriya.dalmia0
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Comment: C: Design matrix for continuous independent variable in limma
... Done, sorry. ...
written 16 months ago by anupriya.dalmia0
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Design matrix for regressing gene expression on a continuous variable - age
... I have 74 samples with log normalised gene counts. I want to see their expression pattern changes with age (range 2-72 years). I am not binning the ages and using them as a continuous variable. This is the script I used to get p-values using splines: require(splines) x<-ns(pheno_UMary$Age, df=5 ...
limma R lmfit design matrix written 16 months ago by anupriya.dalmia0 • updated 16 months ago by Aaron Lun25k
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Comment: C: Design matrix for continuous independent variable in limma
... Hi Aaron, you said that using the spline approach we can look at the results on a "gene-by-gene" basis to interpret the results. How would that be? I am unable to interpret the spline coefficients .... I have run a very similar analysis: This is the script I used to get p-values using splines: req ...
written 16 months ago by anupriya.dalmia0
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Global Trend Analysis using results from EdgeR
... I have generated three DGE lists using the MakeContrasts function in EdgeR for pairwise comparisons of 3 conditions. I now want to make a union of these genes and cluster the expression (preferably, using the k-means algorithm). Following that, I would like to plot the expression profiles of the clu ...
clustering edger consensusclusterplus differential gene expression kmeans written 18 months ago by anupriya.dalmia0 • updated 18 months ago by Aaron Lun25k

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