[BioC] Data filtering

[Anand K.S.Rao [guest]]

Greetings friends!

I seek help with data that I have : 3 time points, 3 genotypes, 3 replicates for each of these = 27 libraries

The goal is to find genes that have different time expression profiles amongst 2 or more genotypes.

After our 1st round of data analysis, (including TMM normalization), the time course graphs and box plots were so noisy in terms of high std error at each time point, that it was hard to say if expression profile of one genotype was overlapping or distinct from that for the other genotypes! R code attached at bottom of this post.

So in short - we now need to employ data filters to check and reduce noise in our data. Some ideas are 
removing genes that have low expression (count) levels
removing genes that have high variance across replicates
removing genes that have low variance across time (constitutively expressed genes are biologically less interesting)

So my question to you is what stage of my analysis do I employ these filters?
On the raw data itself, prior to normalization?
Or should I perform the TMM normalization, use the norm factors to transform my data to non-integer normalized counts and then filter (in which case I think I cannot fit them into negative binomial model, right?)

<CODE>
count = read.table("Input.txt", sep="\t", header=T)                     					
#$#$ read in raw count mapped data

f.count = count[apply(count[,-c(1,ncol(count))],1,sum) > 27,]                               
#$#$ filter ou genes with total read count < 27 across all libraries

f.dat = f.count[,-c(1,ncol(count))]                                                         
#$#$ select only read count, not rest of data frame

S = factor(rep(c("gen1","gen2","gen3"),rep(9,3)))                                           
#$#$ define group

Time = factor(rep(rep(c("0","10","20"),rep(3,3)),3))         								
#$#$ define time

Time.rep = rep(1:3,9)                                                                        
#$#$ define replicate

Group = paste(S,Time,Time.rep,sep="_")                                                         
#$#$ define group_time_replicate

library(edgeR)                                                                              
#$#$ load edgeR package

f.factor = data.frame(files = names(f.dat), S = S , Time = Time, lib.size = c(apply(f.dat,2,sum)),norm.factors = calcNormFactors(as.matrix(f.dat)))  
#$#$  make data for edgeR method

count.d = new("DGEList", list(samples = f.factor, counts = as.matrix(f.dat)))               
#$#$  make data for edgeR method

design = model.matrix(~ Time + S)                                                           
#$#$  make design data for edgeR method

count.d = calcNormFactors(count.d)                                                          
#$#$  Normalize TMM

glmfit.d = glmFit(count.d, design, dispersion = 0.1)                                        
#$#$  Fit the Negative Binomial Gen Lin Models

lrt.count = glmLRT(count.d, glmfit.d)                                                       
#$#$  Likelihood ratio tests

result.count = data.frame(f.count, lrt.count$table)                                         
#$#$  combining raw data and results from edgeR

result.count$FDR = p.adjust(result.count$p.value,method="BH")                               
#$#$  calculating the False Discovery Rate

write.table(result.count, "edgeR.Medicago_count_WT_Mu3.txt",sep="\t",row.names=F)           
#$#$  saving the combined data set
</CODE>

 -- output of sessionInfo(): 

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