Question: Illumina microarray dataset analysis
0
gravatar for amnahsiddiqa
2.5 years ago by
Pakistan
amnahsiddiqa0 wrote:

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.

enter image description here

ADD COMMENTlink modified 2.5 years ago by hrenchert74750 • written 2.5 years ago by amnahsiddiqa0

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

ADD REPLYlink written 2.5 years ago by andrew.j.skelton735.4k

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

ADD REPLYlink written 2.5 years ago by amnahsiddiqa0

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.

ADD REPLYlink written 2.5 years ago by andrew.j.skelton735.4k

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)

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Mike1.1k
0
gravatar for hrenchert747
2.5 years ago by
hrenchert74750
hrenchert74750 wrote:

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

ADD COMMENTlink written 2.5 years ago by hrenchert74750

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

ADD REPLYlink written 2.5 years ago by amnahsiddiqa0

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

ADD REPLYlink written 2.5 years ago by hrenchert74750
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