Question

DEseq Error in checkForExperimentalReplicates

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zhezhenwang • 0

@zhezhenwang-21679

Last seen 5.0 years ago

I had the following error while running DEseq2 comparing groups of different sample size:

Error in checkForExperimentalReplicates(object, modelMatrix) :

The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was deprecated in v1.20 and no longer supported since v1.22.

dds = DESeqDataSetFromMatrix(countData = counts,colData = cli, design = ~ V2)

dds = DESeq(dds)

Here are my cli table and my count matrix

 V1     V2

9 SL70 Sham 1

10 SL71 Sham 2

11 SL72 Sham 3

12 SL73 Sham 4

13 SL74 TAC 1

14 SL75 TAC 2

15 SL76 TAC 3

16 SL77 TAC 4

17 SL78 TAC 5

head(counts)

SL70 SL71 SL72 SL73 SL74 SL75 SL76 SL77 SL78

1 2 2 2 2 4 0 2 6 1

2 1761 2001 1495 1691 1485 1718 1497 1658 1238

3 2060 2234 1494 1505 1261 1776 1670 1256 1249

4 642 722 393 338 724 1436 967 599 936

5 1370 2176 1272 1530 1278 1526 1778 1394 1431

6 326 348 267 301 228 359 328 255 300

I just started using DEseq2, but I did run another comparison, 3 vs 3 samples, with exactly the same code and had no errors

deseq2 • 5.2k views

ADD COMMENT • link 5.0 years ago zhezhenwang • 0

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ADD REPLY • link 5.0 years ago antoniolionader • 0

score 0 · Answer 1 · 2019-11-23

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

I can’t easily see your code or sample table above. The error is pretty literal: that design cannot be fit because there are no replicates: every group in the design has a single sample, and so DESeq2 stops and tells you the problem.

ADD COMMENT • link 5.0 years ago Michael Love 43k

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I have 4 replicates in one group and 5 replicates in another group

ADD REPLY • link 5.0 years ago zhezhenwang • 0

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Take a look at the examples in the vignette and workflow. Or the man pages. You should not name the condition vector control1, control2, control3. That’s not how any of the differential packages label replicates of the control group. Just use “control”.