how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
1
0
Entering edit mode
@husainmanagori1998-22771
Last seen 19 months ago

i have raw read counts of miRNA gene of lung cancer downloaded from GEO. i want to analyze and want to find which genes are differentailly expressed genes among my 90 samples using DESeq2 package. i read about DESeq2 package from bioconductor tutorial and gone through the workflow. but, i didn't understand from where to start with my raw read counts? (also calculated p values)

deseq2 deseq • 324 views
ADD COMMENT
0
Entering edit mode

did you have the normal and and disease(e.g, cancer) dataset or not?

ADD REPLY
0
Entering edit mode

i hve only single file, which has this type of data

ADD REPLY
0
Entering edit mode

To be honest, I suspect that you might be unclear on what "differentially expressed" means.

A gene is called "differentially expressed", if it's expression strength in one type or group of samples is higher than in another type or group. So, you need at least two different groups of samples, so that you can compare one with the other.

ADD REPLY
0
Entering edit mode

Yeah, like @Simon said, you must have at least two types, normally, it includes normal samples and disease samples.

ADD REPLY
0
Entering edit mode

thank you @Simon @ huynguyen96.dnu now i havetwo file, normal file (contain 96 samples), and disease file( samples 96).

ADD REPLY
0
Entering edit mode
Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 13 months ago
Zentrum für Molekularbiologie, Universi…

What do you mean by "differentially expressed"? Please first explain the experimental setup of your study: how do these 90 samples differ from each other?

ADD COMMENT
0
Entering edit mode

these 90 samples differ from each other by raw read counts. file looks like:(miRNA raw read count file)

GeneID sample1 sample2 sample3 sample4 sample5 hsa-let-7a-2-3p 24 15 23 31 19 hsa-let-7a-3p 1031 1050 1155 752 1132 hsa-let-7a-5p 922916.75 1019462.75 1147558.25 1252350.75 797239.25 hsa-let-7b-3p 901 1278 961 530 1144

ADD REPLY

Login before adding your answer.

Traffic: 251 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