User: Achilleas Pitsillides

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Posts by Achilleas Pitsillides

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Comment: C: Unable to create venndiagram using VennDiagram 1.5.1 package
... 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 Pitsillides170
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Answer: A: to find out the union of two sets of genes
... 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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170
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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 Pitsillides170

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