Hi BioC user,
I have a problem extracting the gene set I would like to work with.
Here is I work with my data:
normData <- read.delim("normalizedData.txt",sep ="\t")
######### two class unpaired comparison
# y must take values 1,2
classes <- c(-1,-2,1,2)
#prepere the data for the samr analysis
data.x <-as.matrix(normData[,8:11])
d=list(x=data.x,y=classes,
geneid=as.character(normData[,1]),genenames=as.character(normData[,1]),
logged2=TRUE)
samr.obj<-samr(d, resp.type="Two class paired", nperms=100)
delta.table <- samr.compute.delta.table(samr.obj)
delta=0.4
siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, d,
delta.table,min.foldchange=2)
genes.up <- as.data.frame(siggenes.table$genes.up)
genes.down <- as.data.frame(siggenes.table$genes.lo)
the data set I am working with has four column of two experiments. when
running the samr.compute.siggenes.table command I get
> str(siggenes.table)
List of 5
$ genes.up : chr [1:9769, 1:8] "6587" "865" "22929" "10172" ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ...
$ genes.lo : chr [1:10788, 1:8] "10836" "22277" "1243" "10509"
...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ...
$ color.ind.for.multi: NULL
$ ngenes.up : int 9769
$ ngenes.lo : int 10788
So I guess I have 9769 up-regulated and 10788 down-regulated genes. The
problem is, that not all of them are above 2fold:
> head(siggenes.table$genes.up)
Row Gene ID Gene Name Score(d)
[1,] "6587" "NM_001142426_at" "NM_001142426_at" "670.084615384572"
[2,] "865" "NM_000946_at" "NM_000946_at" "581.731543624152"
[3,] "22929" "NM_147134_at" "NM_147134_at" "469.481132075439"
[4,] "10172" "NM_003640_at" "NM_003640_at" "296.630872483217"
[5,] "10956" "NM_004484_at" "NM_004484_at" "284.233163028334"
[6,] "28444" "XM_001125699_at" "XM_001125699_at" "281.629310344832"
Numerator(r) Denominator(s+s0) Fold Change
[1,] "435.555" "0.650000000000041" "*1.30352619041372e+131*"
[2,] "433.39" "0.745000000000012" "2.90663046260321e+130"
[3,] "248.825" "0.530000000000037" "8.01288059495468e+74"
[4,] "220.99" "0.745000000000012" "3.34671508906627e+66"
[5,] "3059.77" "10.7649999999999" "Inf"
[6,] "163.345" "0.579999999999991" "*1.48506219251034e+49*"
q-value(%)
[1,] "0"
[2,] "0"
[3,] "0"
[4,] "1.95405681104834"
[5,] "1.95405681104834"
[6,] "1.95405681104834"
@What do I need the parameter min.foldchage if it is not a filter to
extract genes with a fold induction value lower than 2?
I would like to know how do I extract a subset of matrix from inside a list?
my siggenes.table is a list with two matrices inside. I would like to filter
these matrices for genes with a 2fold up- and down-regulation.
Thanks
Assa
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] samr_1.28 impute_1.24.0
loaded via a namespace (and not attached):
[1] tools_2.12.0
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