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Question: Pairwise comparasion for multiple conditions using DEXSeq
1
gravatar for chentong_biology
2.0 years ago by
China
chentong_biology10 wrote:

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

 

 

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by chentong_biology10

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

ADD REPLYlink written 2.0 years ago by Alejandro Reyes1.5k

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

ADD REPLYlink written 2.0 years ago by Alejandro Reyes1.5k

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!

ADD REPLYlink modified 3 months ago • written 3 months ago by llo0
0
gravatar for chentong_biology
2.0 years ago by
China
chentong_biology10 wrote:

Alejandro Reyes 

Sorry to hear that. But thanks for your answer and your efforts in developing such great tools.

The 'ADD REPLY' link do not work for me, so I have to give my feedback as an answer. Sorry for the bothering.

Tong Chen

ADD COMMENTlink written 2.0 years ago by chentong_biology10
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