estimazing size factor in DESeq

[frymor]

Hi,

I am using Deseq to analyze my data. I have three replica for each of the two conditions.

When I am running the script in the normal way:

cds = newCountDataSet( Counts_set, condition )
cds = estimateSizeFactors( cds ) # uses the median as location function
cds = estimateDispersions( cds )

I get the following error massage:

[COLOR="Red"]There were 16 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced
2: step size truncated due to divergence
...
[/COLOR]

The dispersion plot looks like that:


but with fitType="local" ot looks like that:


When I am doing the same analysis, but with fitType="local" the warnings disappears.
I read that this happens ,When One is using the analysis without replica, but I have three for each condition.
Is it preferable to run the analysis with local fit type?

What is the meaning of these warnings?

Thanks,
Assa

[dpryan]

For those coming to this late, this was picked up on the Bioconductor email list.