colData design issues, need help in R
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R_diot • 0
@50f26885
Last seen 15 hours ago
Denmark

Hej, im a microbiologist working in my master and I accidently blurted out I took basic bioinformatic as a course and now wants some help with some 39k data entries (my terminology is not the greatest)

Im working on a larger dataset the count matrix looks like this

genes |A.1|A.2|A.3|A.4|B.1|B.2|B.3|B.4|C.1|C.2|C.3|C.4|D.1|D.2|D.3|D.4
AT5G   *imagine a bunch of numbers here
AT6G
AT7G
AT8G
AT9G

coldata <- data.frame(sample = c(rep("A", 4), rep("B", 4), rep("C", 4),rep("D", 4)),
timestamp = c(rep("1",1),rep("2",1),rep("3",1),rep("4",1)))

which looks like this
sample   timestamp
<chr>    <chr>
A       1
A       2
A       3
A       4
B       1
B       2
B       3
B       4
C       1
C       2
C       3
C       4
D       1
D       2
D       3
D       4


and this is my

DESeqDataSetFromMatrix

dds_sub <- DESeqDataSetFromMatrix(countData = count_matrix, colData = coldata, design = ~ sample + timestamp)


as you can se in my resultnames(dds.sub)

resultsNames(dds_sub)
[1] "Intercept"                              "sample_dcp5_vs_Col.0"
[3] "sample_pat1.path1.path2.summ2_vs_Col.0" "sample_summ2_vs_Col.0"
[5] "timestamp_CIM_24hr_vs__NT_0min"         "timestamp_CIM_45min_vs__NT_0min"
[7] "timestamp_CIM_6d_vs__NT_0min"


I only get options for sample or for timestamp

what I need is sample AND timestamp specifically

sample_A.2_VS_B.2


but R keeps spitting this error after me

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, :A 2 and B 2 should be levels of sample such that sample_A.2_vs_A and sample_B.2_vs_A are contained in 'resultsNames(object)'

DESeq2 • 95 views
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@mikelove
Last seen 1 day ago
United States

I'd recommend to pair up with someone who can help you formulate the design and specify how to pull out the right terms. Unfortunately I only have time to help with software related issues here. Besides avoiding errors, you also want to make sure you understand the meaning of the contrasts you are performing.

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I appreciate the help Michael!