Model matrix not full rank

Question: Model matrix not full rank

2.1 years ago by

sally_b86 • 0 wrote:

Dear Michael,

In the following coldata I'm obtaining Model matrix not full rank error. I can't remove the batch effect, I want to take it into consideration. As I concluded its replicates and batch that are a linear combination, when I try the same design without one of them it works normally. And I can't remove the replicate effect as well. Any suggestions?

Thank you.

colData:

	replicate	surgeon	batch	time
Ctl.1	R7	Bruno	a	t0
Ctl.2	R8	Bruno	a	t0
Ctl.3	R2	Lionel	d	t0
Ctl.4	R5	Bruno	c	t0
Ctl.5	R6	Bruno	b	t0
Ctl.6	R1	Bruno	f	t0
Ctl.7	R3	Lionel	g	t0
Ctl.8	R4	Lionel	g	t0
Sham0.1	R7	Bruno	a	t1
Sham0.2	R8	Bruno	a	t1
Sham0.3	R6	Lionel	a	t1
Sham0.4	R3	Lionel	c	t1
Sham0.5	R5	Bruno	c	t1
Sham0.6	R4	Lionel	b	t1
Sham0.7	R1	Lionel	e	t1
Sham0.8	R2	Bruno	e	t1
Sham45.1	R8	Bruno	a	t2
Sham45.2	R7	Bruno	a	t2
Sham45.3	R2	Lionel	d	t2
Sham45.4	R1	Bruno	d	t2
Sham45.5	R3	Lionel	c	t2
Sham45.6	R5	Bruno	c	t2
Sham45.7	R4	Lionel	c	t2
Sham45.8	R6	Bruno	b	t2
Sham24.1	R8	Bruno	a	t3
Sham24.2	R7	Bruno	a	t3
Sham24.3	R1	Bruno	d	t3
Sham24.4	R2	Lionel	d	t3
Sham24.5	R5	Lionel	c	t3
Sham24.6	R4	Bruno	c	t3
Sham24.7	R6	Lionel	b	t3
Sham24.8	R3	Lionel	g	t3

deseq2 model matrix linear combination • 441 views

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modified 2.1 years ago by Michael Love ♦ 26k • written 2.1 years ago by sally_b86 • 0

Answer: Model matrix not full rank

2.1 years ago by

Michael Love ♦ 26k

United States

Michael Love ♦ 26k wrote:

What is the experiment? What are you measuring? What is the design you are currently using? What are you trying to compare or test?

What is the meaning of the replicate column here?

What version of software are you running: include the output of sessionInfo() in posts.

ADD COMMENT • link written 2.1 years ago by Michael Love ♦ 26k

Its a time series experiment to check differential gene expression across time there are many variables like surgeon, biological replicates and library preparation batch that might affect our analysis.

Biological replicates are done in different days.

dds <- DESeqDataSetFromMatrix(countData = cts,
colData = coldata,
design = ~ replicate + batch + surgeon + time)

dds <- DESeq(dds, test = "LRT", reduced = ~ replicate + batch + surgeon )

ADD REPLY • link written 2.1 years ago by sally_b86 • 0

What does R1 share with R1 at other times? Same Q but batch?

ADD REPLY • link written 2.1 years ago by Michael Love ♦ 26k

R1 samples represent the mice sacrificed in the same week. I was wondering if I can remove it from the analysis. Unfortunately, when I do PCA plot, it is clear that there's a variation among biological replicates (8 replicates per time point).

I can consider that its a biological variation and not experimental so once taken into consideration it will induce a big variation right?

ADD REPLY • link written 2.1 years ago by sally_b86 • 0

And what exactly is batch here. What do the batch = a samples have in common?

ADD REPLY • link written 2.1 years ago by Michael Love ♦ 26k

batches correspond to library preparation, the samples that are prepared together for mRNA enrichment.

ADD REPLY • link written 2.1 years ago by sally_b86 • 0

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] DESeq2_1.16.1 SummarizedExperiment_1.6.5 DelayedArray_0.2.7 matrixStats_0.52.2
[5] Biobase_2.36.2 GenomicRanges_1.28.5 GenomeInfoDb_1.12.2 IRanges_2.10.3
[9] S4Vectors_0.14.5 BiocGenerics_0.22.0

loaded via a namespace (and not attached):
[1] genefilter_1.58.1 locfit_1.5-9.1 splines_3.4.1 lattice_0.20-35
[5] colorspace_1.3-2 htmltools_0.3.6 base64enc_0.1-3 blob_1.1.0
[9] survival_2.41-3 XML_3.98-1.9 rlang_0.1.2 DBI_0.7
[13] foreign_0.8-69 BiocParallel_1.10.1 bit64_0.9-7 RColorBrewer_1.1-2
[17] GenomeInfoDbData_0.99.0 plyr_1.8.4 stringr_1.2.0 zlibbioc_1.22.0
[21] munsell_0.4.3 gtable_0.2.0 htmlwidgets_0.9 memoise_1.1.0
[25] latticeExtra_0.6-28 knitr_1.17 geneplotter_1.54.0 AnnotationDbi_1.38.2
[29] htmlTable_1.9 Rcpp_0.12.13 acepack_1.4.1 xtable_1.8-2
[33] scales_0.5.0 backports_1.1.1 checkmate_1.8.4 Hmisc_4.0-3
[37] annotate_1.54.0 XVector_0.16.0 bit_1.1-12 gridExtra_2.3
[41] ggplot2_2.2.1 digest_0.6.12 stringi_1.1.5 grid_3.4.1
[45] tools_3.4.1 bitops_1.0-6 magrittr_1.5 RSQLite_2.0
[49] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.3.4 Formula_1.2-2
[53] cluster_2.0.6 Matrix_1.2-11 data.table_1.10.4 rpart_4.1-11
[57] nnet_7.3-12 compiler_3.4.1

ADD REPLY • link written 2.1 years ago by sally_b86 • 0

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