Hello!
I am new to RNA-seq data analysis :) I downloaded gene expression HTSeq - Counts from TCGAbiolinks of tumor and matched normal sample pairs (54 matched-pairs in total).
Therefore I have a table in which the rows are the ensemble gene ID and the columns are the samples. I would like to know how I should analyze my data (e.g normalization of the data). Where can I find a guideline for getting some suggestions using R?
Thank you in advance
Best
2 answers
DESeq2 has a method implemented called independent filtering, which is called in the standard setting.
Other than that, you can use R functions like which and rowSums to filter your gene count table. I would refrain from that since you remove information used for applying dispersion estimation.
Hi noeD,
if you have access to the bam files, maybe DEWE (http://sing-group.org/dewe/) can be helpful to run the differential expression analysis comparing the to conditions. If you have any doubt, do not hesitate to contact using the online form (http://www.sing-group.org/dewe/contact-us.html).
Regards,
Hugo.
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I think it is helpful for you: EdgeR