Question: How to compare the gene expression signature of Primary tumor cell and normal cancer cell

Question

[Naresh]

How to compare the gene expression signature of Primary tumor cell and normal cancer cell

[mark.ziemann]

Naresh, can you provide some info as to what type of data (RNA-seq/array/other) and what formats they are in now (with a sample), then the nice folks here will be able to help.

[Naresh]

Professor Mark Ziemann, Thank you for your reply. I am a 1st semester PhD student at Seoul National University, Korea. I want to analyze microarray data - to compare primary tumor with that of normal cancer cell and find out the genetic variability in compared with normal and primary tumor,, and then compare it with other databases,, to see the changes in that.. like the same way,, after metastasis..

I don't know how to proceed...

[mark.ziemann]

Please provide some info as to what formats the data are in now (with a sample), and we might be able to help.

[Michael]

This is way to short of a description and wrong. We don't even know if you are looking for data or have your own data.

And what is 'normal cancer cell' in comparison to primary tumor? What do you want to compare?

[alolex]

Naresh, it sounds like you are trying to do a differential expression analysis or are trying to find mutations, but as others have stated, there is not enough information for us to help you. Please review the links provided here differential expression analyses Differential Expression Analysis Theory/Tutorial For The Statistics Layman and here Analysing Microarray Data In Bioconductor, or here for some links to variant calling tutorials Paper Or Detailed Tutorial For Dna Variant Calling Pipeline? Need Help To Start, and read some literature on analyses that are similar to what you want to do. Then come back and expand your question by adding more details on what you are trying to do, how you are currently trying to do it (like what tools), what your data looks like and where you are stuck. Thanks and good luck.