Question: DeSeq2 error: Every gene contains at least one zero, cannot compute log geometric means
0
gravatar for imrankhanbioinfo
5 weeks ago by
Canada/London/Western University
imrankhanbioinfo10 wrote:

Hi there, When I am running the DESeq pipeline on the dds object and getting this error message.

dds_res<-DESeq(dds_PvsN) estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometric means In addition: Warning message: In class(object) <- "environment" : Setting class(x) to "environment" sets attribute to NULL; result will no longer be an S4 object

What strategy should be applied to resolve this conflict?

Thank you very much! Imran

rna-seq • 264 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by imrankhanbioinfo10

Thanks, Kevin and swbarnes2 for your replies,

Kevin your reply was the right solution. This helps us not to remove any sample during this analysis.

So adding a pseudo-count value of '1' to each entry in my data helps to resolve this error.

Best regards: Imran

ADD REPLYlink written 5 weeks ago by imrankhanbioinfo10
3
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe61k
Kevin Blighe61k wrote:

I encountered this error only once in the past. It is as stated: every gene in your data has at least one zero value, and this creates an issue for the size-factor calculation.

Solutions:

  1. add a pseudo-count value of '1' to your data
  2. use: estimateSizeFactors(dds_PvsN, type = 'iterate')

Kevin

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Kevin Blighe61k
0
gravatar for swbarnes2
5 weeks ago by
swbarnes27.8k
United States
swbarnes27.8k wrote:

Check your count matrix. That error can happen if you have a couple of rotten samples. Omitting them might fix things.

ADD COMMENTlink written 5 weeks ago by swbarnes27.8k
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