unreal negative log2fc values
1
0
Entering edit mode
Atul K. • 0
@Atul K.-24477
Last seen 12 days ago
India

Assigning condition and coldata

condition <- factor(c("C","C","C","P","P","P"))
coldata <-data.frame(row.names = colnames(counts_filtered)[-1], condition)

#Deseq
dds<-DESeqDataSetFromMatrix(countData = counts_filtered[, -1],, colData = coldata, design = ~condition)
dds <- DESeq(dds)

#extracting deseq2 results
res <- results(dds, contrast = c ("condition", "C","P"))
res

above is the code I am using to run deseq2. When I look at the results they are different, upregulated genes according to the raw read counts showing me a negative value and the genes which pretty much looks like downregulated in the read counts showing me a positive value. This is between three cases and 3 controls. For example, the read counts of one gene across cases and controls:

C01 C02 C03     P01    P02    P03
14  47  19      129874  25114  31346

and desq results for this gene is as follows:

baseMean                 log2FoldChange

23071.1919508785    -10.843407253606

Can anybody help with this?

DESeq2 des • 124 views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.2k
@atpoint-13662
Last seen 8 hours ago
Germany

I don't see why this is unrealistic. A logFC of -10 is about -1000 on normal scale. The rough difference between the mean of these counts per group (are they normalized?) as roughly in this range. Your contrast is C - P so negative logFCs mean it's higher in P, so this is all in line.

ADD COMMENT

Login before adding your answer.

Traffic: 1010 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