[BioC] maSigPro time problem (2.trial)

[Klaus-Peter Pleissner]

Hello,

we would like to analyze our time course data using maSigPro.
The structure of edesign is following:


 > str(edesign.rna)
int [1:16, 1:3] 30 30 30 30 45 45 45 45 60 60 ...
- attr(*, "dimnames")=List of 2
 ..$ : chr [1:16] "H030A_normalized_r1_ch1" "H030A_normalized_r2_ch1" 
"H030A_normalized_r3_ch1" "H030A_normalized_r4_ch1" ...
 ..$ : chr [1:3] "Time" "Replicate" "Hpy"


The structure of data

 > str(data.rna)
'data.frame':   1280 obs. of  16 variables:
$ H030A_normalized_r1_ch1: num  108.9 121.8 121.8 96 90.5 ...
$ H030A_normalized_r2_ch1: num  131 127 138 117 129 ...
$ H030A_normalized_r3_ch1: num  135 124 117 113 120 ...
$ H030A_normalized_r4_ch1: num  109 105 107 101 103 ...
$ H045A_normalized_r1_ch1: num  99.8 108.9 111.9 81.7 90.8 ...
$ H045A_normalized_r2_ch1: num  102.9 99.2 108.5 104.8 82.3 ...
$ H045A_normalized_r3_ch1: num  109.1 111 118.7 113 93.8 ...
$ H045A_normalized_r4_ch1: num  69.1 82.6 79.6 91.6 76.6 ...
$ H060A_normalized_r1_ch1: num  84.1 NA 91.5 113.7 84.1 ...
$ H060A_normalized_r2_ch1: num  108.8 108.8 100 97.1 88.2 ...
$ H060A_normalized_r3_ch1: num  95.3 79 98 92.6 70.8 ...
$ H060A_normalized_r4_ch1: num  53.1 46.9 87.5 65.6 62.5 ...
$ H075A_normalized_r1_ch1: num  96.4 112.5 112.5 96.4 112.5 ...
$ H075A_normalized_r2_ch1: num  109.1 95.5 115.9 122.7 81.8 ...
$ H075A_normalized_r3_ch1: num  91 91 112 123 91 ...
$ H075A_normalized_r4_ch1: num  45.8 53.4 83.9 83.9 68.6 ...



Using
ts.analysis <- maSigPro(data.rna, edesign.rna)

I got following output

 > ts.analysis <- maSigPro(data.rna, edesign.rna)
[1] "running design"
[1] "running p.vector"
[1] "fitting gene 100 out of 1280"
[1] "fitting gene 200 out of 1280"
[1] "fitting gene 300 out of 1280"
[1] "fitting gene 400 out of 1280"
[1] "fitting gene 500 out of 1280"
[1] "fitting gene 600 out of 1280"
[1] "fitting gene 700 out of 1280"
[1] "fitting gene 800 out of 1280"
[1] "fitting gene 900 out of 1280"
[1] "fitting gene 1000 out of 1280"
[1] "fitting gene 1100 out of 1280"
[1] "fitting gene 1200 out of 1280"
[1] "running T.fit"
[1] "fitting gene 100 out of 322"
[1] "fitting gene 200 out of 322"
[1] "fitting gene 300 out of 322"
[1] "Warning: 76 genes with influential data at slot influ.info. Model 
validation for these genes is recommended"
[1] "running get.siggenes"
[1] "running see.genes  1"
There were 50 or more warnings (use warnings() to see the first 50)


and a Results.pdf -file  in which the first time point is the mean of 
all time points ( mean(c(30,45,60,75)))..
But I want to see each time point separately on the time-axis.

What can be wrong ?

 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base   
other attached packages:
[1] maSigPro_1.16.0 Biobase_2.4.1
loaded via a namespace (and not attached):
[1] limma_2.18.0 Mfuzz_2.2.0



Regards

Klaus-Peter
-- 

Mit freundlichen Grüssen / Best regards

Dr. Klaus-Peter Pleissner
Max Planck Institute for Infection Biology
Core Facility Bioinformatics
Charitéplatz 1
D-10117 Berlin
Germany

*Phone:* +49-30-28460-119
*Fax:*   +49-30-28460-507
*URL:*   http://web.mpiib-berlin.mpg.de/bioinformatik <http://web.mpiib-berlin.mpg.de/bioinformatik/>
*Email:* pleissner at mpiib-berlin.mpg.de  <mailto:pleissner at mpiib-berlin.mpg.de>