EBseq HMM MedianNorm function works and thenEBSeqHMMTest do not

[Diana Duarte]

Hey guys, perhaps this might be a simple question and i do not have many experience. I create object "test" with genes and expression levels like this>

test <- read.table("Genetest.txt", head = TRUE)

then i run this function and it worked

Sizes <- MedianNorm(test)

then i run

EBSeqHMMGeneOut= EBSeqHMMTest(Data=test, sizeFactors=Sizes, Conditions=Conditions,UpdateRd=2)

and this error appear

The input Data is not a matrix


I do not understand why if the first function of the MedianNorm works good... i do not know now why with this seconf function is not possible with the same object. Any idea or suggestion will be very helpful.

[Ning Leng]

Hi Diana,
If you look at str(test) it is probably a data frame instead of matrix.
To convert it to a matrix you can do test2 <- data.matrix(test)
Best,
Ning

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--
Ning Leng, Ph.D
Computational Biologist / Biostatistician
Regenerative Biology Laboratory
Morgridge Institute for Research

[Sakshi Bharti]

Hi,

I have dataset with timepoints each of three replicates:

CondVector <- rep(paste("t",1:16,sep=""),each=3)
uq <- calcNormFactors(x2, method="upperquartile")

EBSeqHMMGeneOut <- EBSeqHMMTest(Data=x2, sizeFactors=uq, Conditions=Conditions, UpdateRd=2)

Output:

Conditions are ordered as:

t1 t2 t3 t4 t5 t6 t7 t8 t9 t10 t11 t12 t13 t14 t15 t16

Estimating parameters when expected FC = 2

iteration time 16.7

The whole process consuming most of the virtual memory on massive machine but still no results. Any solution to speed up the process effectively? 

Thanks!  

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