## User: Adaikalavan Ramasamy

Adaikalavan Ramasamy •

**100**- Reputation:
**100**- Status:
- New User
- Location:
- Last seen:
- 5 years, 11 months ago
- Joined:
- 9 years, 10 months ago
- Email:
- a*********@imperial.ac.uk

#### Posts by Adaikalavan Ramasamy

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... Apologies for cross-posting. Please kindly contact Prof. Lewis
(details below and cc-ed) with any questions regarding the course.
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Announ ...

written 5.9 years ago by
Adaikalavan Ramasamy •

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... 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 8.0 years ago by
Adaikalavan Ramasamy •

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... 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 8.7 years ago by
Adaikalavan Ramasamy •

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... 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 8.7 years ago by
Adaikalavan Ramasamy •

**100**• updated 8.7 years ago by Saroj K Mohapatra •**390**0

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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 9.0 years ago by
Adaikalavan Ramasamy •

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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 9.0 years ago by
Adaikalavan Ramasamy •

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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 9.8 years ago by
Adaikalavan Ramasamy •

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... 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 ...

written 9.9 years ago by
Adaikalavan Ramasamy •

**100**• updated 9.9 years ago by Christos Hatzis •**110**#### Latest awards to Adaikalavan Ramasamy

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