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:
I get the following error massage:
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
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:
Code:
cds = newCountDataSet( Counts_set, condition ) cds = estimateSizeFactors( cds ) # uses the median as location function cds = estimateDispersions( cds )
Code:
[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]
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
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