Format of data matrix, probedata and phenodata for building Rnits object ?
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eu_sanisa • 0
@eu_sanisa-10899
Last seen 5.5 years ago

Hi,

I'd like to analyse my data using Rnits, as it is a sequential in time, but I'm having problems trying to build the Rnits object. I already tried using the ExpressionSet that I build using Biobase and worked perfectly in limma, but it doesn't work. So, my idea would be to build it from the data matrix, probedata and phenodata tables... however, everytime i try it it looks like i have some formatting errors, e.g. the phenodata needs to have columns names "Sample" and "Time". So far I've tried:

data matrix (just showing the first four samples (E19, E23, E24, E07) and four genes):

 E19 E23 E24 E07 1 0.099 0.172 0.115 0.102 2 0.123 0.523 0.544 0.225 3 3.050 3.688 3.250 3.885 4 1.620 2.153 1.926 2.196

probedata (just showing the first four genes):

 ProbeID GeneName 1 1 comp100005_c0_seq1:648-1319 2 2 comp100006_c0_seq1:3-425 3 3 comp100010_c0_seq1:762-1769 4 4 comp100018_c0_seq1:112-666

phenodata (for the first four samples):

 title Time Sample E19 7 1 E23 5 1 E24 3 1 E07 3 1

To import the tables (all saved as tab delimited), i use the normal read.table command, so, so far my script looks like:

# phenodata:
phenodata <- as.data.frame(tmp)

# probedata:
probedata <- as.data.frame(tmp)

# data matrix:
obj <- as.matrix(tmp)

# build Rnits object:

rnitsobj = build.Rnits(obj, probedata = probedata, phenodata = phenodata, logscale = TRUE, normmethod = 'Between')

Error in build.Rnits(obj, probedata = probedata, phenodata = phenodata,  :
Phenotype data table must have the same column names as data table

What are the right formats for the data matrix, probedata and phenodata?

Eugenia

Rnits microarray limma • 633 views
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It is a requirement that rownames(phenodata) == colnames(obj).  You will have to set the rownames of the phenodata and load header information into the obj so the colnames get set.

phenodata <- read.table("phenodata.txt", row.names=1)
obj <- as.matrix(tmp)

You may run into some other issues as it looks like Rnits also requires Time to be unqiue.