## User: Achilleas Pitsillides

Achilleas Pitsillides •

**170**- Reputation:
**170**- Status:
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- Location:
- Last seen:
- 6 years, 10 months ago
- Joined:
- 8 years, 11 months ago
- Email:
- a****@virginia.edu

#### Posts by Achilleas Pitsillides

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... As Wenhuo said your numbers as miscalculated. The intersection of
groups 1,
2, 3 has 227 elements (n123=227) one element more than the
intersection of
2 and 3 (n23 =226) which is impossible.
I hope this helps.
cheers,
Achilleas
On Fri, Nov 9, 2012 at 11:51 AM, wenhuo hu wrote:
> Though I can ...

written 6.9 years ago by
Achilleas Pitsillides •

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... Hi Priya,
One way to do that is to use vennCounts and vennDiagram from the limma
package. If you got your results from limma then you can just follow
the
manual page for the function; otherwise you can do something along
these
lines: I am assuming that your significant results reside in two
matrice ...

written 6.9 years ago by
Achilleas Pitsillides •

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Answer:
A: Fwd: covariate information

... Dear Chol-hee,
The short answer is that the two model matrices are different and they
have
different dimensions; you can verify this by using the dim(mod_mat) to
see
the dimension of the model matrix.
Here is my understanding: If you have a factor f1 with 3 levels and a
factor f2 with 2 levels (w ...

written 6.9 years ago by
Achilleas Pitsillides •

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Answer:
A: permutation loop

... Hey,
I don't think this is the most efficient way to do this but here it
goes:
#Create a random names vector with some repeated names
names.col <- sample(paste("name",1:4,sep =""),10,replace=T)
print(names.col)
#Now find all pairs that are the same
temp <- sapply(names.col,rep,length(names.c ...

written 7.8 years ago by
Achilleas Pitsillides •

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Comment:
C: cosine similarity

... Hi,
I am not sure if there is a package for this but assuming that your
data is
A=[a1,a2,a3,a4...,an] in rows.
Then,
%A=matrix(rnorm(50),nr=5) %testing case 1
%A=matrix(rep(1,100),nr=5) %testing case 2
myDist=function(A){
intermediateRes1=A%*%t(A)
myVec=sqrt(diag(
intermediateRes1))
intermediateRes2 ...

written 8.2 years ago by
Achilleas Pitsillides •

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Comment:
C: CGHcall

... Hi,
I think there is a typo in the guide (The error just says that there
is no
such function loaded). The correct command would have been
make_cghRaw
cheers,
Achilleas
On Thu, May 26, 2011 at 11:34 AM, Sean Davis
wrote:
> Hi, Yan.
>
> You'll need to provide the output of sessionInfo().
& ...

written 8.3 years ago by
Achilleas Pitsillides •

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Comment:
C: paired sample LIMMA

... Hi Elliott,
I don't know anything about your experiment so I can't help much more
than
the Limma guide would.
I guess if you are interested in expression changes between State1
and
State2 (for all the mice and all the cycles) and between cycle 1 and
cycle 2
(for all the mice and all the cycles).
co ...

written 8.3 years ago by
Achilleas Pitsillides •

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Answer:
A: paired sample LIMMA

... Hi,
In your current design the variables MouseX ( for X in {2,3,4})
encode the
difference of MouseX from Mouse1, i.e. the intercept is Mouse1. If you
want
to have Mouse1 be explicit then just change:
pairdesign <- model.matrix(~MouseNo+Cycle+State, ref = "ref")
to
pairdesign <- model.matrix(~ ...

written 8.3 years ago by
Achilleas Pitsillides •

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Comment:
C: Average based on group

... Ok I get it now,
If your data is as shown i.e. sorted, then can you just create a dummy
variable:
rep(1:10,n) where n is the number of groups and then use by or tapply?
So in your example:
by(df[,4],rep(1:10,2),mean)
cheers,
Achilleas
On Thu, May 12, 2011 at 12:38 PM, Fabrice Tourre
wrote:
> T ...

written 8.4 years ago by
Achilleas Pitsillides •

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Answer:
A: Average based on group

... Hi,
Assuming I understood the question correctly you can use the "by"
function
from the base package i.e:
by(MyData[,4],MyData[,2],mean)
where the factor is in the second column and the numerical data is in
the
fourth column.
cheers,
Achilleas
On Thu, May 12, 2011 at 11:20 AM, Fabrice Tourre
wrote ...

written 8.4 years ago by
Achilleas Pitsillides •

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