Illumina microarray dataset analysis

Question

[ASid]

I have to analyze an illumina microarray data set. i have pasted the image of the data i have regarding it. usually we see aveg signal ,stdeerr, p detection value etc in illumin achip data. but this has only avg signal and p detection value for each sample . How I can analyze this data. I have already tried to read it through beadarray and lumibatch file command but there are errors.

[andrew.j.skelton73]

I'd advise you go back to the company/ people that ran the arrays and ask for the raw data.

[ASid]

Alright but for example that is not the possibility then what I can do with it.

[andrew.j.skelton73]

With the example you've illustrated, it all depends on how it was generated, and even then there probably isn't enough information there for a typical robust analysis, if this is raw data. Is this raw or normalised data? It might be useful to include more context in your post, i.e. where you got the data from, what analyses you want to perform, etc.

[Mike]

Mostly Illumina array data contains ControlProbeProfile.txt & SamplelProbeProfile.txt file and some other raw files, You can use limma tool with these two files, your file format is Ok, ControlProbeProfile.txt & SamplelProbeProfile.txt has only avg signal and p detection value for each sample.

see limma manual (https://www.bioconductor.org/packages/3.3/bioc/vignettes/limma/inst/doc/usersguide.pdf)

example:

17.3 Comparing Mammary Progenitor Cell Populations with Illumina BeadChips

library(limma)

dataFile <- "data/SampleProbeProfile.txt"

qcFile <- "data/ControlProbeProfile.txt"

(reference; http://www.gettinggeneticsdone.com/2014/12/importing-illumina-beadarray-data-into-r.html)

Answer 1

[hrenchert747]

I did it using Expander software and MeV, you can also try JMP Genomics and Biocinductor R if able to program somehow.

[ASid]

Alright I will try that and posy back if it works. Thak you

[hrenchert747]

best w., it surely works, you can also try Cytoscape with plugins for networks from microarrays, pay attention to the proper data input, all other things are to push buttons there