Dear all!

 

When I use LIMMA to analyze microarray data, I use Array Weight parameter. I
have some questions about it.

 

The command is:

#array weight

arrayw <- arrayWeights(MAbe, design, weights=MAbe$weights)

arrayweights <- targets

for (m in 1:narrays){arrayweights$arrayw[m] <- arrayw[[m]]}

write.table(arrayweights, file = file.path(resultdir,
"arrayweights_BewteenArray.txt"),sep="\t", dec = ".",row.names= FALSE)

# combine array and spot weights

library(statmod)

W <- matvec(MAbe$weights, arrayw)

# Fit linear models

fit <- lmFit(MAbe, design, method="ls", weights=W)

# Compute contrast of interest

cont.matrix <- makeContrasts (HvsL=L-H, levels=design)

               fit2 <- contrasts.fit(fit, cont.matrix)

fit2 <- eBayes (fit2)

# Toptable, remember to change name of generated files according to contrast

toptable <- topTable(fit2,number=10000, adjust.method = "fdr")

DE <- toptable$adj.P.Val[toptable$adj.P.Val<0.05]

length(DE)

# 2285

toptable <- topTable(fit2, number=2285, adjust.method = "fdr", sort.by="p")

write.table(toptable, file = file.path( resultdir,
"2285_between_ArrayWeight_fdr_CD8.txt"),sep="\t", dec = ".",row.names=
FALSE)

 

My questions are:

 

(1) How is Log2(Fold Change) in the toptable gotten?     

If I don't use array weight, I can get log2(fold change) by (M(l)-M(h)). But
when I use array weight, I don't know how to get it?

 

(2) How to get the M value that is used in lmFit analysis?  

         I know how to get the M value after normalization. I use this
command.

#loess normalize in arrays

MAin <- normalizeWithinArrays(RG, method="loess", weights=RG$weights,
bc.method="none")

# write normalised data to TMEV-file - for clustering

# Tab Delimited, Multiple Sample Files (TDMS) (*.txt)

mMin <- MAin$M

colnames(mMin) <- paste(colnames(mMin),targets$Pig,sep=".")

clusterdata <- cbind(MAin$genes,mMin)

FnameOutput <- file.path(resultdir,"Index_MAin_slides.txt")

write.table(clusterdata, file=FnameOutput, sep="\t", row.names=FALSE)

       When I use array weight, I guess M value will be changed. Is it that?

 

Thanks a lot for your attention!

 

Best wishes,

 

Yu GAO

 

 


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