Question: DESeq2 analysis of two tissues with 3 different conditions
0
gravatar for mark.pekarsky
12 days ago by
mark.pekarsky20 wrote:

Hi, these are my very first steps in RNAseq and for the first time in my life I am trying to use a DESeq2 package in R, and I am trying to figure out how can I "sort" my results if I have two tissues (intestine and brain) and for each tissue I have 3 conditions - "control", "black" and "white". Means I have a column "tissue" (for intestine and brain) and I have "state" (for my 3 conditions)

If I understood it well - I have to start from that:

dds <- DESeqDataSetFromMatrix(
countData = GeneCounts,
colData = colData,
design = ~ tissue + state )

dds <- DESeq(dds) 

res <- results(dds)

That would be the "default" way but when I am trying to do

res1 <- results(dds, contrast=c("tissue","white","control"))

for example for the "white-control" pair I have the following error message:

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues,  : 
  white and control should be levels of tissue such that tissue_white_vs_brain and tissue_control_vs_brain are contained in 'resultsNames(object)'

Can anyone please explain what that suppose to mean?

Thank you!

rna-seq deseq2 R • 69 views
ADD COMMENTlink modified 12 days ago by swbarnes27.0k • written 12 days ago by mark.pekarsky20
0
gravatar for swbarnes2
12 days ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:

Reading the vignettes and tutorials is not enough. You need to work through examples. You also need to ask yourself "exactly what am I trying to compare to what?" Because that results command makes no sense.

ADD COMMENTlink modified 12 days ago • written 12 days ago by swbarnes27.0k
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: 1157 users visited in the last hour