[BioC] SAM and siggenes packages

[perin]

Hi,

Thanks.
I download and install the new version of siggenes. I also added the two 
lines of code to set s0 as the median of the standard deviations of the 
gene and it's working now.
But, I still have a pb: I played with 6 replicates as a test but I 
planned to generate only 4 replicates (2 dye swap) for  each step of my 
time course experiment. So if I try with only 4 replicates instead 6 I 
gave the output as follow:

SAM Analysis for the one-class case.
 
Warning: There are 8448 genes which have variance Zero or no non-missing 
values.
         The d-value of these genes is set to NA.
 
There are 8448 missing d values.
 
Error in "[<-"(*tmp*, int, value = numeric(0)) :
        nothing to replace with
In addition: Warning messages:
1: no finite arguments to min; returning Inf
2: no finite arguments to max; returning -Inf

with the following code:

a<-median(rs.cal(salt_stress,1:4,B=1)$s)
sam.output<-sam(maM(salt_stress,salt_cl,s0=a)

Again, any idea ? (I tried with only 5 replicates and it's working ???)


 


Holger Schwender a écrit:

>Hi,
>
>the warning message says that all the expression values of each of the 353
>genes are either the same or NAs.
>
>The error message usually occurs in the computation of the fudge factor when
>there are less than 101 different d values. This "bug" will be fixed in the
>next version of siggenes. You can avoid this error message by setting s0 in
>sam(...) to a reasonable value, or by doing something like
>
>  
>
>>a<-median(rs.cal(salt_stress,1:6,B=1)$s) 
>>sam(salt_stress,salt_cl,s0=a)
>>    
>>
>
>This will specify the fudge factor as the median of the standard deviations
>of the genes.
>
>Since you have >8000 genes this error message shouldn't actually occur. So
>another idea is that you might have an old version of siggenes in which the
>one-class analysis did not work correctly. If you don't have the siggenes
>version of the developmental section of Bioconductor, you should download
>this version (1.0.6).
>
>Best,
>Holger
>
>  
>
>>Hi,
>>
>>I'am new on this mailing list and I probably have a 'stupid' question.
>>I'am doing SAM analysis for the one-class case on a 6 replicates per 
>>8448 gene matrix.
>>I get each time this message
>>
>>SAM Analysis for the one-class case.
>> 
>>Warning: There are 353 genes which have variance Zero or no non-missing 
>>values.
>>         The d-value of these genes is set to NA.
>> 
>>Error in var(v) : missing observations in cov/cor
>>
>>Any idea ?
>>
>>Here the code:
>>
>>sam.output<-sam(salt_stress,salt.cl)
>>
>>where salt.cl<-c(rep(1,6))
>>and salt_stress a matrix (6 col per 8448 row)
>>
>>
>>thanks
>>
>>
>>
>>
>>Thanks
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>>
>>    
>>
>
>  
>


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