Hi list.

I am having problems with carrying out quantitative analysis with samr. I am trying to correalte gene expression across a microarray data set with weight loss. My expression data is in the form of a matrix and my weight loss data is in the form of a vector. Toy examples (but real data) follow.

#expression data

wld2

 V1   V2   V3   V4   V5
[1,] 7.90 7.57 7.45 8.09 7.67
[2,] 7.60 7.23 7.17 7.64 7.21
[3,] 8.24 7.78 7.67 8.29 7.75
[4,] 9.60 9.18 9.08 9.71 9.20
[5,] 9.31 8.93 8.79 9.39 8.97
 
class(wld2)
[1] "matrix"

wlv2

 wlv2
[1] 16.5 17.1  8.1 22.4  0.0

class (wlv2)
[1] "numeric"

The two other parameters are a character list of geneids and a character list of genenames.

I have put these components together as detailed in the samr vignette.

d=list(wld2, wlv2, geneid, genenames)

And attempted sam anaylsis as follows:

sam.obj <- samr(d, resp.type='Quantitative', nperms=100)

This fails with the following errors:

Error in x %*% yy : requires numeric matrix/vector arguments
In addition: Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

I know that %*% is the matrix multiplication operator but my x (wld2) and y (wlv2) values are defined as they should be (matrix and vector respectively) and I cannot track down my mistake.

Can anyone help?

Thank you - session info follows.

Iain

R version 2.6.2 (2008-02-08) 
i486-pc-linux-gnu 

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_1.12.2       RCurl_0.8-3          samr_1.25           
[4] impute_1.0-5         affy_1.16.0          preprocessCore_1.0.0
[7] affyio_1.6.1         Biobase_1.16.2      

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 XML_1.93-2 







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