[BioC] Coefficients not estimable

[Naomi Altman]

The problem is that donor is nested within gender.  The only way I am 
aware of to handle this in limma is to use donor as a block.

Regards,
Naomi


At 11:24 AM 2/7/2012, somnath bandyopadhyay wrote:


>  Dear Gordon and limma users,
>
>I am trying to fit a linear model to assess variability in healthy 
>donors over days for both genders using Affymetrix microarray data. 
>I am interested in assessing variability arising from geneder, day 
>of blood donated and individual donors. When I tried to do a linear 
>fit in using limma, I am not able to assess the coefficients for 
>gender.System is computationally singular for the gender main 
>effect. Is there any way to assess the variability arising from all 
>three main effects? Any help would be greatly appreciated.
>
>Following is my target file:
>
>
>
>
>
>
>
>
>Array_NUID
>gender
>day
>donor
>
>NUID.0000.0133.2260
>male
>d1
>M1
>
>NUID.0000.0133.2261
>male
>d2
>M1
>
>NUID.0000.0133.2262
>male
>d8
>M1
>
>NUID.0000.0133.2230
>female
>d1
>F2
>
>NUID.0000.0133.6809
>female
>d2
>F2
>
>NUID.0000.0133.2251
>female
>d8
>F2
>
>NUID.0000.0133.2228
>female
>d15
>F2
>
>NUID.0000.0133.2229
>female
>d28
>F2
>
>NUID.0000.0133.2231
>female
>d1
>F3
>
>NUID.0000.0133.2232
>female
>d2
>F3
>
>NUID.0000.0133.2233
>female
>d8
>F3
>
>NUID.0000.0133.2234
>female
>d15
>F3
>
>NUID.0000.0133.2265
>male
>d1
>M4
>
>NUID.0000.0133.2267
>male
>d8
>M4
>
>NUID.0000.0133.2268
>male
>d15
>M4
>
>NUID.0000.0133.2269
>male
>d28
>M4
>
>NUID.0000.0133.2236
>female
>d1
>F5
>
>NUID.0000.0133.2237
>female
>d2
>F5
>
>NUID.0000.0133.2238
>female
>d8
>F5
>
>NUID.0000.0133.6810
>female
>d15
>F5
>
>NUID.0000.0133.2240
>female
>d28
>F5
>
>NUID.0000.0133.2270
>male
>d1
>M6
>
>NUID.0000.0133.2271
>male
>d2
>M6
>
>NUID.0000.0133.2272
>male
>d8
>M6
>
>NUID.0000.0133.2273
>male
>d15
>M6
>
>NUID.0000.0133.2274
>male
>d28
>M6
>
>NUID.0000.0133.2241
>female
>d1
>F7
>
>NUID.0000.0133.2242
>female
>d2
>F7
>
>NUID.0000.0133.2243
>female
>d8
>F7
>
>NUID.0000.0133.2244
>female
>d15
>F7
>
>NUID.0000.0133.2245
>female
>d28
>F7
>
>NUID.0000.0133.2246
>female
>d1
>F8
>
>NUID.0000.0133.2247
>female
>d2
>F8
>
>NUID.0000.0133.2248
>female
>d8
>F8
>
>NUID.0000.0133.2249
>female
>d15
>F8
>
>NUID.0000.0133.2250
>female
>d28
>F8
>
>
>Following is the code I am using:
>library("limma")
>rna <- read.table('qced_non_redundant_rma_data.txt', header=T, 
>row.names=1, sep= "\t")
>annotation <- read.table('Test_Samples_Annotation.txt', header=T, 
>row.names=1, sep= "\t")
>## rearrange the annotations to conform to the RMA data
>annotation <- annotation[colnames(rna),]
>## check that the annotations and data match
>if (sum(sort(rownames(annotation)) == sort(colnames(rna))) != 
>length(rownames(annotation))) {
>   stop ("ERROR: annotation rownames and RMA colnames do not match")
>}
>donor <- factor(annotation$donor)
>day <- factor(annotation$day)
>gender <- factor(annotation$gender)
>design <- model.matrix(~ donor + gender + day, data=annotation)
>fit <- lmFit(rna,design)
>fit2 <- eBayes(fit)
>write.fit(fit,file="effects.txt",digits=30, adjust="BH", 
>method="separate",sep="\t")
>
>
>
>Following is my sessionInfo:
> > sessionInfo()
>R version 2.10.1 (2009-12-14)
>x86_64-unknown-linux-gnu
>locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>attached base packages:
>[1] stats     graphics  grDevices utils     datasets  methods   base
>other attached packages:
>[1] limma_3.2.3
>loaded via a namespace (and not attached):
>[1] tools_2.10.1
>         [[alternative HTML version deleted]]
>
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