Count table statistical analysis

Question

[ToTheMoon]

Hi, I have a count table (14200x200)(rows: genes, cols: samples). I normalized the row count table with Deseq2. What would be some of the best statistical analyses on this count table? what type of measurements can be statistically important or have meaningful results.

Thanks!

[ATpoint]

What are the data, what is the analysis goal?

[swbarnes2]

Someone spent time and money to generate this data. They likely had questions they wanted answered. Ask the submitters.

[Ram]

Please keep in mind that posting the same question to multiple sites can be perceived as bad etiquette, because efforts may be made to address a problem that has already been solved elsewhere in the meantime.

The helpful thing to do if you do decide to post on multiple forums is to add a link to the other forum posts on each post so people will look at the other posts before investing their effort.

Link to post on bioinfo SE: https://bioinformatics.stackexchange.com/questions/22168/statistical-analysis-on-count-table

Answer 1

[ToTheMoon]

I searched and found the below link to be very useful. https://hbctraining.github.io/Training-modules/planning_successful_rnaseq/lessons/sample_level_QC.html

[Ram]

That page is wrong. You cannot use TPM for between-sample comparisons. RNA-seq analysis produces relative measures, so there will always be caveats to between-sample comparisons.