Dear Mahdi,

a well-established tool is MeV (https://sourceforge.net/projects/mev-tm4/files/). It user-friendly and includes all important statistical tests, clustering techniques and visualization tools.

M

There are free spread-sheet programs that can do this job, like for instance OpenOffice Calc.

If you have large amounts of calculations and want some automatation you should consider R (www.r-project.org). For R there are add-on packages that are specialized on the analysis of gene-expression data (from qPCR, NGS, ...). You may have a look at the BioConductor projects (https://www.bioconductor.org/packages/release/BiocViews.html#___Technology).

Hi ... u can use REST program by determining the control and treatment for genes and ur target gene 

Download it is easy

Dear Mahdi,

a well-established tool is MeV (https://sourceforge.net/projects/mev-tm4/files/). It user-friendly and includes all important statistical tests, clustering techniques and visualization tools.

M

Have you tried Image J?

Dear Mahdi

If you don't have a control group then you cannot calculate any relative expression, 

Relative gene expression is RELATIVE because you need a control group or sample to calculate it and you get results in term of fold changes versus your control.

You may use a GSEA analysis (or GSA), look how to do it in internet, but you should to have control-case genes in pairs genes to compare:

http://software.broadinstitute.org/gsea/index.jsp

My advice is only compare the genes that you have in both conditions.

Another good online bioinformatic suit is babelomics v4 and v5:

V4:

http://v4.babelomics.org/

V5:

http://babelomics.bioinfo.cipf.es/

Use R languaje is the best way to do bioinformatic studies, but you should to learn how to write in R.

BTW, ImageJ is only for image analysis, such as images obtained from microscopy, not for gene expression.

Godspeed!!!