[BioC] Communicating gene-probe relationships to sam

[Seth Falcon]

Hi Charles,

Charles Crane <ccrane at purdue.edu> writes:
>     I am trying to use sam to identify single-feature polymorphisms between
> two barley cultivars.  I am running Bioconductor 1.7, Biobase 1.8.0, affy
> 1.8.1, and siggenes 1.4.0 under Mac OS X 10.3.9.
> probe-level data from my CEL files, background correct the pm values with
> rma, quantile normalize, and isolate the pm intensities in a data frame, but
> both sam and sam.snp consistently and instantly fail with "Error in
> FUN(data, cl, ...) : There should be at least 25 samples."  This happens
> even though there are 22840 genes and 11 probes per gene in the
> data. 

But how many samples?  If I'm reading your transcript correctly, it
looks like you have 20 samples and as the method is telling you, it
wants 25.  I realize this isn't all that helpful, but I suspect the
limitation is based on the statistical properties of the method.

>     Thank your very much for your time.  Also, do you plan to include
> directions for using sam for SNP analysis, going all the way from ReadAffy
> through sam for a case history, in a future vignette?  It would save the
> uninitiated a lot of time and frustration.

That would make a great contributed document (hint, hint) :-)

> +  sampleNames = c("000113_5hr_kindered_H20_inoc_2x2",
> "000114_12hr_kindered_H20_inoc_3bx1", "000122_5hr_peruvian_H20_inoc_14bx1",
> +  "000123_12hr_peruvian_H20_inoc_15bx1",
> "000141_Non-host-resistant-barley_16bx2", "000157_24hr_Kindered_H2O_Inoc_1",
> +  "000158_0hr_Kindered_H2O_Inoc_4",
> "000159_0hr_Kindered_S_passerini_inoc_5", "000161_0hr_Peruvian_H2O_inoc_13",
> +  "000162_0hr_Peruvian_S_passerini_17", "000189_0hr_403-rep2_H2O_inoc_21b",
> "000190_5hr_403-rep2_H2O_inoc_22b",
> +  "000191_12hr_403-rep2_H2O_inoc_23b", "000192_24hr_403-rep2_H2O_inoc_24b",
> "000193_0hr_403-rep2_inoc-s_pass_25b",
> +  "000201_0hr_405-rep2_H2O_inoc_33b", "000202_5hr_405-rep2_H2O_inoc_34b",
> "000203_12hr_405-rep2_H2O_inoc_35b",
> +  "000204_24hr_405-rep2_H2O_inoc_36b",
> "000205_0hr_405-rep2_inoc-s_pass_37b"),

Here it looks like you have 20 samples.  Do the docs explain anything
about the 25 sample requirement?  

Hope that helps,

+ seth