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Tony
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@tony-15866
Last seen 6.6 years ago
Which are the steps to get significantly up regulated and down regulated genes from samples which are not replicates?
By doing this step "dds <- DESeq(dds)" I am getting a warning message "same number of samples and coefficients to fit..."
Is it possible to get different combination results? The input will be multiple samples read count in a single file.
Okay. Which are the steps we have to use to get up regulated and down regulated genes?
Please take a look at our workflow:
http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
Is there any difference between old DESeq and DESeq2 in calculating the up and down regulated genes?
This is answered in our papers and specifically in the vignette, see the Table of Contents. Please take some time to read over our documentation before posting. I want to focus my time on support questions not covered in the publications and documentation.