DESeq2 time series
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@pavelabaffy-10944
Last seen 5.3 years ago

Hello, Here is lot of about RNA-Seq time course experiments so I have chaos. If is somewhere correct answer for me, please send me link.

 

I have time course experiment - 3 condition - 1 control + 2 treated, and 4 times

LibraryName                     countf condition time
1    WT-0-mpw-B     WT-0-mpw-B_union.count        WT    0
2    WT-0-mpw-D     WT-0-mpw-D_union.count        WT    0
3   WT-30-mpw-A    WT-30-mpw-A_union.count        WT   30
4   WT-30-mpw-D    WT-30-mpw-D_union.count        WT   30
5   WT-60-mpw-C    WT-60-mpw-C_union.count        WT   60
6   WT-60-mpw-D    WT-60-mpw-D_union.count        WT   60
7   WT-90-mpw-B    WT-90-mpw-B_union.count        WT   90
8   WT-90-mpw-D    WT-90-mpw-D_union.count        WT   90
9  TRIM-0-mpw-A   TRIM-0-mpw-A_union.count      TRIM    0
10 TRIM-0-mpw-B   TRIM-0-mpw-B_union.count      TRIM    0
11 TRIM-30-....  TRIM-30-mpw-A_union.count      TRIM   30
12 TRIM-30-....  TRIM-30-mpw-B_union.count      TRIM   30
13 TRIM-60-....  TRIM-60-mpw-A_union.count      TRIM   60
14 TRIM-60-....  TRIM-60-mpw-B_union.count      TRIM   60
15 TRIM-90-....  TRIM-90-mpw-A_union.count      TRIM   90
16 TRIM-90-....  TRIM-90-mpw-B_union.count      TRIM   90
17 enNOS-0-....  enNOS-0-mpw-A_union.count     enNOS    0
18 enNOS-0-....  enNOS-0-mpw-D_union.count     enNOS    0
19 enNOS-30.... enNOS-30-mpw-B_union.count     enNOS   30
20 enNOS-30.... enNOS-30-mpw-D_union.count     enNOS   30
21 enNOS-60.... enNOS-60-mpw-C_union.count     enNOS   60
22 enNOS-60.... enNOS-60-mpw-D_union.count     enNOS   60
23 enNOS-90.... enNOS-90-mpw-A_union.count     enNOS   90
24 enNOS-90.... enNOS-90-mpw-C_union.count     enNOS   90

I want compare changes in gene expression during time (I don't care about differences at time 0). What is correct design for DESeq2 to find theese genes?

(For example - 1 gene in control have maximum expression at time 30 and after that, expression rapidly decrease, but in treated samples expression of theese gene is still increased. But at the time 0 - in sample TRIM expression level is simillar with WT and in sample enNOS is increased.)

Thanks.

deseq2 timecourse • 2.5k views
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@mikelove
Last seen 36 minutes ago
United States

You need to be able to phrase your biological question as a specific statistical test. For example, if you follow the time series example in the RNA-seq workflow, you can obtain genes which have differences in their time-series profile across condition. This is a typical and straightforward analysis. However, you can also perform other analyses, for example, using the VST or rlog to transform the data to the log scale, and then clustering genes by their time expression profile. We do not have a pipeline for such exploration, but it's relatively simple using base R commands.

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