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Hi, I have a question about DEXSeq package for analyzing multiple samples. Like the sample information listed below. I have six samples loaded as DEXSeqDataSets. Default, every sample will be compared with the first sample known as Col0 here.
I wonder if there is any function to extract pairwise comparasion results as res <- results(dds, contrast=c("conditions", "Col3", "Col24")) in DESeq2.
Thanks!
Tong Chen
> sample
conditions cell time
Col0_1 Col0 Col 0
Col0_2 Col0 Col 0
Col3_1 Col3 Col 3
Col3_2 Col3 Col 3
Col24_1 Col24 Col 24
Col24_2 Col24 Col 24
cbf0_1 cbf0 cbf 0
cbf0_2 cbf0 cbf 0
cbf3_1 cbf3 cbf 3
cbf3_2 cbf3 cbf 3
cbf24_1 cbf24 cbf 24
cbf24_2 cbf24 cbf 24
> colData(dxd)
DataFrame with 24 rows and 6 columns
sample conditions cell time exon sizeFactor
<factor> <factor> <factor> <factor> <factor> <numeric>
1 Col0_1 Col0 Col 0 this 0.9126171
2 Col0_2 Col0 Col 0 this 0.9458306
3 Col3_1 Col3 Col 3 this 0.8914356
4 Col3_2 Col3 Col 3 this 1.2490106
5 Col24_1 Col24 Col 24 this 0.9687948
... ... ... ... ... ... ...
20 cbf0_2 cbf0 cbf 0 others 1.0687401
21 cbf3_1 cbf3 cbf 3 others 0.9824029
22 cbf3_2 cbf3 cbf 3 others 1.0701895
23 cbf24_1 cbf24 cbf 24 others 0.9257264
24 cbf24_2 cbf24 cbf 24 others 1.1723387
> dds <- DEXSeqResults(dxd)
> dds
<numeric> <numeric> <numeric>
XLOC_000002+XLOC_004161:E001 10.882663 10.44266 10.388549
XLOC_000002+XLOC_004161:E002 20.561282 20.03267 22.448874
XLOC_000002+XLOC_004161:E003 9.510509 10.14679 9.860588
XLOC_000002+XLOC_004161:E004 10.871525 11.25257 10.929886
XLOC_000002+XLOC_004161:E005 14.204665 13.51434 13.703109
... ... ... ...
XLOC_032817+XLOC_032818+XLOC_032742:E008 4.024608 4.100783 2.736283
XLOC_032817+XLOC_032818+XLOC_032742:E009 2.848699 2.606964 1.367766
XLOC_032820:E001 NA NA NA
XLOC_032821:E001 NA NA NA
XLOC_032823:E001 NA NA NA
cbf0 cbf3 cbf24
<numeric> <numeric> <numeric>
XLOC_000002+XLOC_004161:E001 8.553736 9.334228 9.814653
XLOC_000002+XLOC_004161:E002 18.986580 19.484306 23.109959
XLOC_000002+XLOC_004161:E003 9.409119 9.513795 11.259645
XLOC_000002+XLOC_004161:E004 10.103124 11.030351 12.261620
XLOC_000002+XLOC_004161:E005 12.996807 13.718990 15.307747
... ... ... ...
XLOC_032817+XLOC_032818+XLOC_032742:E008 3.850081 3.421292 4.39521544
XLOC_032817+XLOC_032818+XLOC_032742:E009 2.061519 1.715996 0.05112219
XLOC_032820:E001 NA NA NA
XLOC_032821:E001 NA NA NA
XLOC_032823:E001 NA NA NA
log2fold_Col3_Col0 log2fold_Col24_Col0
<numeric> <numeric>
XLOC_000002+XLOC_004161:E001 -0.05954207 -0.067037538
XLOC_000002+XLOC_004161:E002 -0.03757565 0.126712863
XLOC_000002+XLOC_004161:E003 0.09342863 0.052151148
XLOC_000002+XLOC_004161:E004 0.04970028 0.007724016
XLOC_000002+XLOC_004161:E005 -0.07187362 -0.051861600
... ... ...
XLOC_032817+XLOC_032818+XLOC_032742:E008 0.02705116 -0.5566307
XLOC_032817+XLOC_032818+XLOC_032742:E009 -0.12793236 -1.0584817
XLOC_032820:E001 NA NA
XLOC_032821:E001 NA NA
XLOC_032823:E001 NA NA
log2fold_cbf0_Col0 log2fold_cbf3_Col0
<numeric> <numeric>
XLOC_000002+XLOC_004161:E001 -0.34740516 -0.2214290920
XLOC_000002+XLOC_004161:E002 -0.11495013 -0.0776176400
XLOC_000002+XLOC_004161:E003 -0.01546295 0.0004983823
XLOC_000002+XLOC_004161:E004 -0.10575280 0.0209244683
XLOC_000002+XLOC_004161:E005 -0.12820759 -0.0501904871
... ... ...
XLOC_032817+XLOC_032818+XLOC_032742:E008 -0.06395915 -0.2343070
XLOC_032817+XLOC_032818+XLOC_032742:E009 -0.46659536 -0.7312565
XLOC_032820:E001 NA NA
XLOC_032821:E001 NA NA
XLOC_032823:E001 NA NA
log2fold_cbf24_Col0
<numeric>
XLOC_000002+XLOC_004161:E001 -0.1490225
XLOC_000002+XLOC_004161:E002 0.1685845
XLOC_000002+XLOC_004161:E003 0.2435668
XLOC_000002+XLOC_004161:E004 0.1735953
XLOC_000002+XLOC_004161:E005 0.1078971
... ...
XLOC_032817+XLOC_032818+XLOC_032742:E008 0.1270858
XLOC_032817+XLOC_032818+XLOC_032742:E009 -5.8002097
XLOC_032820:E001 NA
XLOC_032821:E001 NA
XLOC_032823:E001 NA
Hi Tong Chen,
Thanks for your interest in DEXSeq!
Specifying contrasts is not implemented in DEXSeq. If you want to do pairwise comparisons, you would need to subset the DEXSeqDataSet based on the conditions that you want to compare and then rerun DEXSeq on the DEXSeqDataSet containing this subset.
Alejandro
Hi Tong Chen,
Thanks for your interest in DEXSeq!
Specifying contrasts is not implemented in DEXSeq. If you want to do pairwise comparisons, you would need to subset the DEXSeqDataSet based on the conditions that you want to compare and then rerun DEXSeq on the DEXSeqDataSet containing this subset.
Alejandro
Hello, I am also interested in doing a pairwise condition with DEXSeq. How would I subset the DEXSeqDataSet? I have 2 conditions, 3 replicates each, and 3 stages. Overall, 18 different samples. My data set looks like this:
condition stage
GFP_18_1 GFP 18
GFP_18_2 GFP 18
GFP_18_3 GFP 18
GFP_28_1 GFP 28
GFP_28_2 GFP 28
GFP_28_3 GFP 28
GFP_38_1 GFP 38
GFP_38_2 GFP 38
GFP_38_3 GFP 38
ICD_18_1 ICD 18
ICD_18_2 ICD 18
ICD_18_3 ICD 18
ICD_28_1 ICD 28
ICD_28_2 ICD 28
ICD_28_3 ICD 28
ICD_38_1 ICD 38
ICD_38_2 ICD 38
ICD_38_3 ICD 38
I would like to compare GFP 18 vs ICD 18, GFP 28 vs ICD 28, etc. How would I subset this and what would be my design matrix, currently I am using ~sample + exon + stage:exon + condition:exon. Thank you!