Defining conditions in EBSeq-HMM

Question

[zizigolu]

Excuse me,

I have cell lines treated with lead (pb) from day 1 to day 26 and 26 match controls (52 samples without replicates). I was trying EBSeqHMM for my time series so;

> CondVector <- rep(paste(c("C", "L"),1:52,sep=""),each=1)

> View(CondVector)


**Conditions <- factor(CondVector, levels=c("C1", "C3", "C5", "C7", "C9", "C11", "C13", "C15", "C17", "C19", "C21", "C23", "C25", "C27", "C29", "C31", "C33", "C35", "C37", "C39", "C41", "C43", "C45", "C47", "C49", "C51", "L2", "L4", "L6", "L8", "L10", "L12", "L14", "L16", "L18", "L20", "L22", "L24", "L26", "L28", "L30", "L32", "L34", "L36", "L38", "L40", "L42", "L44", "L46", "L48", "L50", "L52"))**

> Sizes <- MedianNorm(as.matrix(raw.processed))

> EBSeqHMMGeneOut <- EBSeqHMMTest(as.matrix( raw.processed), sizeFactors=Sizes, Conditions=Conditions,  UpdateRd=2)



 Conditions are ordered as:

 C1 C3 C5 C7 C9 C11 C13 C15 C17 C19 C21 C23 C25 C27 C29 C31 C33 C35 C37 C39 C41 C43 C45 C47 C49 C51 L2 L4 L6 L8 L10 L12 L14 L16 L18 L20 L22 L24 L26 L28 L30 L32 L34 L36 L38 L40 L42 L44 L46 L48 L50 L52

 Estimating parameters when expected FC = 2


 iteration time 45.1

Error in rep.intrep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :

  invalid 'times' value

>

I also tried

> Conditions <- factor(CondVector, levels=c("C1", "C2", "C3", "C4", "C5", "C6", "C7", "C8", "C9", "C10", "C11", "C12", "C13", "C14", "C15", "C16", "C17", "C18", "C19", "C20", "C21", "C22", "C23", "C24", "C25", "C26", "L1", "L2", "L3", "L4", "L5", "L6", "L7", "L8", "L9", "L10", "L11", "L12", "L13", "L14", "L15", "L16", "L17", "L18", "L19", "L20", "L21", "L22", "L23", "L24", "L25", "L26"))
> 

> EBSeqHMMGeneOut <- EBSeqHMMTest(as.matrix(GeneMat), sizeFactors=Sizes, Conditions=Conditions,
+                                 UpdateRd=2)

 Conditions are ordered as: 
 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 L1 L2 L3 L4 L5 L6 L7 L8 L9 L10 L11 L12 L13 L14 L15 L16 L17 L18 L19 L20 L21 L22 L23 L24 L25 L26
 Estimating parameters when expected FC = 2 
Error in EBTest_ext(Data = tmpdata, NgVector = NgVector, Conditions = Cond.use,  : 
  Less than 2 conditions - Please check your input

May one who is familiar with EBSeq-HMM please help me to figure out how define my conditions?? I want to identify my up or down regulated genes in day points

Thanks a lot in advance

[g.subashika]

Hi did u find a solution for this??

[zizigolu]

Sorry no I gave up on that :(