DESeq normalization
1
0
Entering edit mode
nafsa • 0
@05efe0b6
Last seen 10 weeks ago
Canada

Enter the body of text here

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
Hi, I`d like to normalize my dataset with DESeq2. I make the DESeq object with : dds = phyloseq_to_deseq2(ps, Design) followed by deseq_counts_vst = varianceStabilizingTransformation(dds).
And I get error saying every gene contains at least one zero, cannot compute log geometric means.
Now i want to use pseudocount. Although I don`t know how to write the script. Could you please help?
flowCHIC • 135 views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 47 minutes ago
United States

In my opinion, this type of data is not appropriate for DESeq2 scaling methods (or inference), which are developed for RNA-seq. If there are no genes without a zero, the median ratio method will not work.

ADD COMMENT

Login before adding your answer.

Traffic: 159 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6