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Old 11-27-2011, 03:52 PM   #1
coralgirl
Junior Member
 
Location: BC

Join Date: Nov 2011
Posts: 6
Default DESeq Plot Error

Hi,

I'm trying to plot the scatterplot of direct vs. moderated log-ratios and I keep getting an error:

Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf

This is what I have put in:

> cdsBlind <- estimateDispersions( cds, method="blind" )
> vsd <- getVarianceStabilizedData( cdsBlind )
> mod_lfc <- (rowMeans( vsd[, conditions(cds)=="treated", drop=FALSE] ) -
+ rowMeans( vsd[, conditions(cds)=="untreated", drop=FALSE] ))
> lfc <- res$log2FoldChange
> finite <- is.finite(lfc)
> table(as.character(lfc[!finite]), useNA="always")

-Inf Inf NaN <NA>
83 212 285 0
> largeNumber <- 10
> lfc <- ifelse(finite, lfc, sign(lfc) * largeNumber)
> plot( lfc, mod_lfc, pch=20, cex=.3,
+ col = ifelse( finite, "#80808040", "red" ) )

Is it because I am running analysis on samples with no replicates? (I know - not good, but it's all that I have...). Any ideas? Thanks.
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Old 11-28-2011, 01:07 AM   #2
Wolfgang Huber
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Location: Heidelberg, Germany

Join Date: Aug 2009
Posts: 109
Default

Dear Coral Girl

it looks like your mod_lfc consists of all non-finite values. What are the conditions names in your object cds? Note that in the line
Quote:

mod_lfc <- (
rowMeans( vsd[, conditions(cds)=="treated", drop=FALSE] ) -
rowMeans( vsd[, conditions(cds)=="untreated", drop=FALSE] ))
you select columns in the data matrix with the names treated and untreated, and if there are no such columns, rowMeans will return NaN. In this case, you need to modify the above code according to your condition names.

Hope this helps.
Wolfgang
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Old 11-29-2011, 10:35 AM   #3
coralgirl
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Posts: 6
Default

Hi Wolfgang,

Thank you very much - that was exactly the problem. A rookie mistake on my behalf!
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