Question: DESeq2 problem with resultsNames
0
gravatar for baffiak1902
2.3 years ago by
baffiak190210
baffiak190210 wrote:

Hi, can somebody explain me, where I make mistakes?

I have DESeq sample table:

 SampleName                 countf condition replicate
1       15_3A 15_3A_union_name.count         A         3
2       15_3B 15_3B_union_name.count         B         3
3       15_3C 15_3C_union_name.count         C         3
4       15_3D 15_3D_union_name.count         D         3
5       15_3E 15_3E_union_name.count         E         3
6       20_7A 20_7A_union_name.count         A         7
7       20_7B 20_7B_union_name.count         B         7
8       20_7C 20_7C_union_name.count         C         7
9       20_7D 20_7D_union_name.count         D         7
10      20_7E 20_7E_union_name.count         E         7
11      20_8A 20_8A_union_name.count         A         8
12      20_8B 20_8B_union_name.count         B         8
13      20_8C 20_8C_union_name.count         C         8
14      20_8D 20_8D_union_name.count         D         8
15      20_8E 20_8E_union_name.count         E         8
16      20_9A 20_9A_union_name.count         A         9
17      20_9B 20_9B_union_name.count         B         9
18      20_9C 20_9C_union_name.count         C         9
19      20_9D 20_9D_union_name.count         D         9
20      20_9E 20_9E_union_name.count         E         9

and I've runed DESeq2

dds=DESeqDataSetFromHTSeqCount(samplesDESeq,directory="directory/to/count/",design= ~replicate + condition)

after that, I analyzed it by DESeq function

dds <- DESeq(cds)

But, when I wanted compare everything with condition A, i cannot find conditionA in resultsNames

> resultsNames(dds)
[1] "Intercept"  "replicate3" "replicate7" "replicate8" "replicate9" "conditionB" "conditionC" "conditionD" "conditionE"

Where is a problem?

Thanks.

rna-seq deseq2 • 899 views
ADD COMMENTlink modified 2.3 years ago by Devon Ryan88k • written 2.3 years ago by baffiak190210
2
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

Condition A is the intercept.

ADD COMMENTlink written 2.3 years ago by Devon Ryan88k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1303 users visited in the last hour