I'm studying R and I like to repeat published works, like this: Bioinformatics analysis of gene expression profile data to screen key genes involved in pulmonary sarcoidosis.
but in these protein-protein interactions works they do not give much informations abous how was analyzed, they say only the genes with the | log2fold change (FC) | > 1 and FDR <0.05 were considered the SDRs.
This paper used this GSE16538 from Crouser ED, Culver DA, Knox KS, Julian MW et al. Gene expression profiling identifies MMP-12 and ADAMDEC1 as potential pathogenic mediators of pulmonary sarcoidosis. Am J Respir Crit Care Med 2009 May 15;179(10):929-38
My questions are:
- These articles (PPI network) usually don't repeat the analyzes with the same parameters of the original paper, why?
- Because they don1t use the same parameters they find differentresults and this influences the networks, so I should or not repeat the parameters of the original paper?
- Now, in relation to my studies with R, even using the same cutoff parameters, I often ddon't find the same numbers of genes of the article, should I be doing something wrong? or does this happen even because of the few information about the R code used?