Question: I would like to analyse microarray samples
1
gravatar for Sabine
4.8 years ago by
Sabine60
India
Sabine60 wrote:

I have two samples with me. they are CEL files. image file form microarray studies. I would like to analyse and determine the differentially expressed genes . Now my question is anybody please tel me how can i analyse the microarray CEL files?

and is there any free softwares available for this kind of analysis?

 thank you

 

 

test microarray de • 1.4k views
ADD COMMENTlink modified 4.5 years ago • written 4.8 years ago by Sabine60
1

I can assure you that this is not the right way to get help in any online community. As a rule of thumb, if your question consists of a single sentence you are doing it wrong.

You need to provide much more detail about your data and protocols, and most importantly you need to make an effort yourself and try to define your experimental question. I am not yet talking about choice of software or method at all. 

Please read: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Michael Dondrup46k

I am not aware of Illumina producing cel files, they might be affymetrix cel files, are you sure about the files origin? Do you know anything about the experimental conditions in the study, how many replicates do you have?

ADD REPLYlink written 4.8 years ago by Michael Dondrup46k

Yes this is from affymetrix, total i have 2 files 

ADD REPLYlink written 4.8 years ago by Sabine60

Really? How can i analyse these 2 and give  atleast a ranking by determining the top genes .thanks

ADD REPLYlink written 4.8 years ago by Sabine60

and is there any free softwares available for this kind of analysis?

ADD REPLYlink written 4.8 years ago by Sabine60
1

please do not make an answer use the add comment button. There is ample free software out there, there are also ample lists of free microarray software out there, here is one: http://pathology.wustl.edu/research/cores/lcg/index.php?page=Microarray%20Data%20Analysis

I recommend R/Bioconductor or dChip (https://sites.google.com/site/dchipsoft/)

ADD REPLYlink written 4.8 years ago by Michael Dondrup46k

thank you..let me tryy

ADD REPLYlink written 4.8 years ago by Sabine60
3
gravatar for Michael Dondrup
4.8 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

If you have only two samples without replication it is not possible to perform a proper DE analysis using statistical tests. The only thing you can do is rank the genes by absolute differences between those two samples, extracting the top N genes and use them for further evaluation.

ADD COMMENTlink written 4.8 years ago by Michael Dondrup46k
2
gravatar for Sabine
4.5 years ago by
Sabine60
India
Sabine60 wrote:

i have prepared normalised data as excel using Bioconductor .How can i determine the possible list of genes from that?

I have used 2 methods for the normalization, namely RMA and mas5

 

ADD COMMENTlink written 4.5 years ago by Sabine60
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