User: Adaikalavan Ramasamy

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Posts by Adaikalavan Ramasamy

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13th MRC Social, Genetic & Developmental Psychiatry SUMMER SCHOOL 18th - 22th June 2012
... Apologies for cross-posting. Please kindly contact Prof. Lewis (details below and cc-ed) with any questions regarding the course. ---------------------------------------------------------------------- ---------------------------------------------------------------------- ------------------ Announ ...
genetics written 5.7 years ago by Adaikalavan Ramasamy100
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Answer: A: Fisher's method of combining p-values
... The statistics from Fisher's method simply sums up the p-values on log scale across the studies and multiplied by minus two. Under the null hypothesis, this follows a chisquare distribution with degrees of freedom equivalent to twice the number of studies. If you store the p-values from different s ...
written 7.8 years ago by Adaikalavan Ramasamy100
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Answer: A: Beta score of DNA methylation assays
... Sonia Shah, thanks for the link. The Beta score is calculated as you said with the addition that any negative values of Cy3 and Cy5 are set to zero. Sean Davis, thanks for pointing out to the methylumi package. It looks like a nice package. I am slightly concerned that you are analyzing the Beta sc ...
written 8.5 years ago by Adaikalavan Ramasamy100
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Beta score of DNA methylation assays
... Hi there, I been handed a tabular file from DNA methylation containing "Beta" values (rows are CpG island and columns are subjects) from Illumina platform. The Beta values range between 0 and 1. I am wondering how this "Beta" value is derived, what it means and how to use it. Or do I calculate th ...
written 8.5 years ago by Adaikalavan Ramasamy100 • updated 8.5 years ago by Saroj K Mohapatra390
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Answer: A: Curious file size issues
... I am not an expert in R data representations. However, my experience suggests that if an object is stored incorrectly as matrix instead of data.frame, then the object sizes may be bloated. Also if it is a data.frame, check that each column is stored correctly - via matrix(obj). E.g. storing numeric ...
written 8.7 years ago by Adaikalavan Ramasamy100
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Comment: C: ANOVA p value calculation
... Assumin that columns 1-3 represents the first cell line, columns 4-6 represents second cell line etc, then you can try something like cellline <- factor( paste("type_", rep(1:17, each=3), sep="") ) apply( Data, 2, function(gene) anova(lm(gene ~ cellline))$"Pr(>F)"[1] ) However, in the co ...
written 8.7 years ago by Adaikalavan Ramasamy100
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Comment: C: Merging microarray datasets
... This is an interesting question and one that I like to explore further. The papers I have seen on combining microarray datasets so far select one algorithm for Affymetrix and one algorithm for cDNA. Has anyone investigated which combination of preprocessing algorithm(s) make data from these two pl ...
written 9.6 years ago by Adaikalavan Ramasamy100
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published studies with technical replicates
... Hi, I am trying to estimate the variability technical replicates from different microarray platforms. The few papers I found on this topic and current opinion seems to suggest that technical replicates are not required for microarrays. However, I like to estimate the distribution of variablity of ...
microarray written 9.6 years ago by Adaikalavan Ramasamy100 • updated 9.6 years ago by Christos Hatzis110

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