[BioC] limma: coefficient not estimable when dataset reduced by a few samples

[Natasha Sahgal]

Dear List,

I have array data for 42 tumorBT - tumorAT patients. Initial analysis
(adding patient and batch covariates to the model) I managed to obtain a
list of DE genes.

However now, I need to reduce this set of 42 to 33 patients pairs and
reanalyse the data. This time though it seems that it can't estimate the
coefficient of one patient, would this not affect my results as NA
coefficients are produced?

What I do not understand is what has changed for this to happen now? How
do I rectify it?

Code:
dim(tum.dat.red)
27555 66 

## Overall Sample Descriptions
>batch = as.factor(t.info.red$Batch)
batch
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 2 2
[39] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
Levels: 1 2


>treat = droplevels(t.info.red$Status_Treatment)
>treat = as.factor(treat, levels=c("Tumour_BT", "Tumour_AT"))
treat
[1] Tumour_AT Tumour_BT Tumour_BT Tumour_AT Tumour_AT Tumour_BT Tumour_BT
 [8] Tumour_AT Tumour_BT Tumour_AT Tumour_AT Tumour_BT Tumour_BT Tumour_AT
[15] Tumour_BT Tumour_AT Tumour_AT Tumour_BT Tumour_BT Tumour_AT Tumour_BT
[22] Tumour_AT Tumour_AT Tumour_BT Tumour_BT Tumour_AT Tumour_BT Tumour_AT
[29] Tumour_BT Tumour_AT Tumour_AT Tumour_BT Tumour_BT Tumour_AT Tumour_AT
[36] Tumour_BT Tumour_BT Tumour_BT Tumour_BT Tumour_BT Tumour_BT Tumour_BT
[43] Tumour_BT Tumour_BT Tumour_AT Tumour_AT Tumour_AT Tumour_AT Tumour_AT
[50] Tumour_AT Tumour_AT Tumour_AT Tumour_BT Tumour_BT Tumour_BT Tumour_BT
[57] Tumour_BT Tumour_BT Tumour_BT Tumour_AT Tumour_AT Tumour_AT Tumour_AT
[64] Tumour_AT Tumour_AT Tumour_AT
Levels: Tumour_BT Tumour_AT


>patient = as.factor(t.info.red$Trial.number)
patient
 [1] 13 25 13 25 18 28 18 28 30 39 30 53 39 53 32 42 32 51 42 51 34 45 34
55 45
[26] 55 54 54 37 57 37 57 35 52 35 52 17 7  12 10 14 11 16 15 14 16 15 17
7  12
[51] 10 11 20 26 36 40 48 23 24 23 20 24 26 36 40 48
33 Levels: 7 10 11 12 13 14 15 16 17 18 20 23 24 25 26 28 30 32 34 35 36
... 57


## Deisgning model with BATCH effect
>design.tum = model.matrix(~treat+batch+patient)

## Fit model  & make contrasts
> fit.tum <- lmFit(tum.dat.red, design.tum)
Coefficients not estimable: patient57
Warning message:
Partial NA coefficients for 27555 probe(s)


sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] limma_3.12.0

loaded via a namespace (and not attached):
[1] tools_2.15.0



Many Thanks in advance,
Natasha