few significant genes from DESeq2 analysis
1
0
Entering edit mode
Ming • 0
@2dddf277
Last seen 6 weeks ago
United States

Hi , I'm trying to get DEG from the old and young group with DESeq2, but there are no significant genes. the adjusted p values are very close to 1. Could someone help me find out the problem?

here are my count data and coldata

 Gene Small_Intestine_34_m_3  Small_Intestine_22_m_18 Small_Intestine_56_m_21

1 0610005C13Rik                    477                     639                     760

2      Trappc2b                    215                     179                     187

3 0610009L18Rik                     12                      18                      12

4         Sanbr                     93                      59                     101

5 0610010K14Rik                     14                      17                      34

6      Ncbp2as2                    537                     552                     470


 tissue age sex age_sex               sample_id agegroup

Small_Intestine_34_m_3  Small_Intestine   3   m     3_m  Small_Intestine_34_m_3    young

Small_Intestine_22_m_18 Small_Intestine  18   m    18_m Small_Intestine_22_m_18      old

Small_Intestine_56_m_21 Small_Intestine  21   m    21_m Small_Intestine_56_m_21      old

Small_Intestine_41_m_1  Small_Intestine   1   m     1_m  Small_Intestine_41_m_1    young

Small_Intestine_8_m_15  Small_Intestine  15   m    15_m  Small_Intestine_8_m_15      old

Small_Intestine_24_f_3  Small_Intestine   3   f     3_f  Small_Intestine_24_f_3    young

dds <- DESeqDataSetFromMatrix(countData=expr_filt2, 
                              colData=subset_md, 
                              design=~agegroup, tidy = TRUE)
#run DESeq2
dds$agegroup <- relevel(dds$agegroup, ref="old")
dds <- DESeq(dds)

#store/view results
res <- results(dds)
DESeq2 • 180 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 16 hours ago
United States

there are no significant genes. the adjusted p values are very close to 1. Could someone help me find out the problem?

The data are telling you something.

ADD COMMENT

Login before adding your answer.

Traffic: 613 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