Dear Bioconductor Scientists,
I am rather new to NGS data analysis, I learned what I know all by myself as there is no bioinformaticians where I work.
Nevertheless, I already analyzed my own affymetrix HTA 2.0 data, as well as a couple public data on affymetrix HGU133 and Illumina HumanHT12 V3/4 microarrays (and should analyze some Agilent 4x44K soon). In the past I also got my hand on Chip-seq/RNA-seq data, and learned the basics (but it's been some time, I hope it's just like bike, you never really forget it ;) ).
I am working on an immune cell subtype, which can be schematized this way :
Primary cells are extracted from blood, let's call them the O cells. They can be differentiated into A, B and C subtypes (and more).
The trouble with public data is the inconsistency in the differentiation methods, the poor number of replicates, the fact that controls are not the same (sometimes fresh O cells, sometimes O cells cultivated with only medium for the same time, sometimes no controls...). So I figured out that it would make sense to combine all these data in a meta analysis to gain power. And maybe also add RNAseq results from similar experiments for an increased precision.
The results I would like to obtain are :
- Identify genes differentially expressed in specific conditions (A, B or C against O, B/C against A), either in all studies or in a majority of studies.
- Identify gene expression profiles of A, B and C in order to find potentially similar cells enrichment in cancer tissues data (microarray/RNA-seq)
For now, I read some literature (10.1371/journal.pmed.0050184;10.1186/1471-2105-14-368), found some packages (crossmeta, GeneMeta, metaArray, MetaOmics), but as I have limited statistical knowledge, the explications are somewhat obscure to me here, as to what method (p-value vs effect size vs rank ?) is best suitable for my purpose.
I guess my questions for you dear members are :
- Is this kind of analysis (as I explain it) possible ? Even for neophyte ?
- What are your advices on how to perform this ? Which packages do you recommend ? Could you share some experience on similar subjects ?
Thank you for your time,