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
[[alternative HTML version deleted]]
Manca Marco (PATH)
2011-Feb-09 16:54 UTC
[R] R: [BioC] samr - extract genes from siggenes.table
I am not sure about this... I think they have logFC larger than 2... you are simply seeing them in scientific notation. Why don't you try setting the option scipen (penalty for scientific notation) "on the high side"? Something like:> options(scipen = 50)should be more than enough... Anyway, most likely other people can give you better hints. All the best, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************************************************************* This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************************************************************* ________________________________________ Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Assa Yeroslaviz [frymor at gmail.com] Inviato: mercoled? 9 febbraio 2011 17.35 A: bioconductor; R help forum Oggetto: [BioC] samr - extract genes from siggenes.table 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor