resultsNames(dds) is not similar to coldata(dds)?
Entering edit mode
A.J. ▴ 20
Last seen 19 months ago
United States

I have a dds object with these coldata:

> head(colData(dds_RNA))

DataFrame with 6 rows and 9 columns
         Sample     Subject    Batch Generation    Genotype        Area      Sex    Group sizeFactor
    <character> <character> <factor>  <numeric> <character> <character> <factor> <factor>  <numeric>
2B2         2B2         2B2        A        244          TT         ACB        F    NACTT   0.530504
3B1         3B1         3B1        A        243          CC         ACB        M    NACCC   0.701971
3D1         3D1         3D1        A        244          TT         ACB        M    NACTT   0.617343
3E2         3E2         3E2        A        244          TT         ACB        F    NACTT   0.844923
4B2         4B2         4B2        A        251          CC         ACB        F    NACCC   1.004906
4C3         4C3         4C3        A        252          CC         ACB        F    NACCC   0.848526

But if I do

> resultsNames(dds_RNA)
 [1] "Intercept" "Group1"    "Group2"    "Group3"    "Group4"    "Group5"    "Sex1"      "Batch1"    "Batch2"    "Batch3"    "Batch4"   

I don't understand why. I was used to see that it would give me Group_NACTT_NACCC options, and I have no clue why it all of a sudden changed into this. I mean, why is it giving Group1 and Group2 names?

If I try

>resultsNames(dds_RNA, name = "Group_NACTT_vs_NACCC")

Error in resultsNames(dds_RNA, name = "Group_NACTT_vs_NACCC") : 
  unused argument (name = "Group_NACTT_vs_NACCC")

Similary, using a contrast results in errors as welll? I am very confused as it has always been working. Help would be appreciated!

DESeq2 • 385 views
Entering edit mode
A.J. ▴ 20
Last seen 19 months ago
United States

I cleared my workspace and started everything again, problem solved!


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