[BioC] SAM and siggenes packages
perin
perin at cirad.fr
Wed Apr 28 10:04:57 CEST 2004
Hi,
Thanks a lot. Now, sam function is working but (sorry for that !), there
is now a problem with sam.plot. Everything seems ok except for sam.plot
gene list output
Here is the code (I tried with golub dataset for this example):
golubvf<-golub[,1:4]
golubvf.cl<-c(1,1,1,1)
a<-median(rs.cal(golubvf,1:4,B=1)$s)
sam.output<-sam(golubvf,golubvf.cl,s0=a)
sam.final<-sam.plot(sam.output,d=1.4)
Error in inherits(x, "data.frame") : subscript out of bounds
It draws the sam plot for d=1.4 but nothing in sam.final
Christophe
>Oh, sorry I've forgot: Please source the attached code to R. Then it should
>work. There was another bug in the one-class case which I've fixed only for
>the next version of siggenes which will appear soon (when Release 1.4 of
>Bioconductor comes out).
>
>I've also attached the next version of the function fudge which can handle
>less than 101 genes.
>
>
>
>>So I did it:
>>
>>here are the last lines
>>
>>
>>[8347] 0.084854730 0.148227947 0.106908754 0.125831287 0.077950147
>>0.211227137
>>[8353] 0.152660230 0.045091101 0.096348186 0.044063845 0.108855645
>>0.092417888
>>[8359] 0.118671164 0.027960521 0.043253745 0.046361978 0.154575781
>>0.152634900
>>[8365] 0.074517075 0.229593012 0.082204362 0.206090376 0.045857296
>>0.094095230
>>[8371] 0.103852101 0.233859308 0.258523505 0.103864178 0.122385598
>>0.167787555
>>[8377] 0.168447995 0.095190885 0.095376051 0.049927168 0.053458959
>>0.102979050
>>[8383] 0.183686758 0.162928860 0.101409564 0.055026031 0.047275238
>>0.299989073
>>[8389] 0.048762658 0.114255858 0.213818969 0.065428394 0.012298578
>>0.061579019
>>[8395] 0.050404750 0.075257078 0.084360630 0.199929845 0.177594221
>>0.157630579
>>[8401] 0.180217253 0.112000120 0.218196589 0.152459139 0.144681365
>>0.073595428
>>[8407] 0.108158061 0.013548077 0.149060865 0.123811131 0.308569776
>>0.217594634
>>[8413] 0.071042281 0.099095831 0.029147566 0.044104928 0.109420584
>>0.116411330
>>[8419] 0.121903308 0.053624854 0.159189549 0.203203948 0.128026072
>>0.142591910
>>[8425] 0.140158370 0.095307900 0.230283970 0.182668313 0.159248974
>>0.215344233
>>[8431] 0.128684507 0.126580411 0.067487608 0.041372752 0.076218630
>>0.118931153
>>[8437] 0.292739641 0.058138725 0.057913610 0.108836945 0.125646992
>>0.194450518
>>[8443] 0.092050998 0.926009673 0.164894890 0.304727643 0.415619179
>>0.174991675
>>
>>So standard deviations seems not to be equal to zero....
>>
>>I tried also with another set of expression data (golub) using the first
>>four columns, five six and 12 and gave a similar result.
>>
>>It's working (one class) until five replicates and gave a similar error
>>that I got with my data if I worked with four replicates or less ?
>>
>>Strange ?
>>
>>Thanks
>>
>>Best regards
>>
>>Dr Christophe Perin
>>
>>
>>Holger Schwender a écrit:
>>
>>
>>
>>>It seems that each gene has the same value for each of the four
>>>
>>>
>>replicates
>>
>>
>>>(because of the error message). Otherwise all the expression values of
>>>
>>>
>>the
>>
>>
>>>genes have to be NAs. Please take a look on the standard deviations by
>>>
>>>
>>>
>>>
>>>
>>>>rs.out<-rs.cal(salt_stress,1:4,B=1)
>>>>rs.out$s
>>>>
>>>>
>>>>
>>>>
>>>Are they all zero? If yes, then all genes have the same value for each of
>>>their expression levels.
>>>
>>>
>>>
>>>
>>>
>>>>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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