Closed:How I deal with this expression set
1
0
Entering edit mode
AZ ▴ 30
@fereshteh-15803
Last seen 10 months ago
United Kingdom

Hi

I have gene expression raw counts like this

          A1 B1   C1     D1  E1  F1
A2M     511 1623 665    208 553 469
AADAT   34  137 372     7   52  124
ABCB1   119 114 123    22   25  89
ABCB11  27  186 200    27   30  49
ABCC2   1   10  21     1    8   3

For each patients I also have some characteristics like percent of infiltrating immune cells (IC) and tumor cells (TCs), etc like below

> head(meta)
    IC PD.L1 TC TILs TILs.group
A1  3     1  3    0          2
B1  2     1  0    0          1
C1  2     1  0    0          2
D1  0     0  0    0          2
E1  1     0  0    1          3
F1  0     0  0    0          1
>

I want differentially expressed genes, but I can not figure out how to let all of these meta data in my design

Can you help me please?

Thank you

deseq2 r • 113 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 686 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