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:
tmp <- read.csv("phenodata.txt")
phenodata <- as.data.frame(tmp)

# probedata:
tmp <- read.csv("probedata.txt")
probedata <- as.data.frame(tmp)

# data matrix:
tmp <- read.table("datamatrix.txt")
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?

Thanks in advance for your help,

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) 
tmp <- read.table("datamatrix.txt", header=TRUE) 
obj <- as.matrix(tmp)

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

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