Hi everybody, I'm totally new in this field , I come from Software Engineering. I'm doing the first things such as Differential Expression Analysis with gene expression data and so on. I have already followed a curated tutorial on how to retrive data from GEO in R and did an analysis with gene expression data. But now My task is to "play" with platelet data and I have a reference number with which , using GeoQuery, I retrieved the matrix with all the info. The problem is that here I cant access the data in detail as I could with gene expression data. I know , I may sound stupid but I don't know how to retrive deep information about the experiment ( in the pdf they talk about differential mRNA expression in platelet in the experiment data) because for example using the function fData(data) , that I used previously to retrive expression data on the previous experiment, returns me null. When I use the function summary(exprs(data))) it returns me the GSM with no further info , instead in the gene expression data I had the mean value ecc.. . I think is because being platelet data the things are different, can I ask how to study this kind of data, like really the generic things used to analyse this data?
Title : RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics ( Experiment type Expression profiling )
summary(exprs(platelet_experiment)) :
GSM1662534 GSM1662535 GSM1662536 GSM1662537 GSM1662538
Mode:logical Mode:logical Mode:logical Mode:logical Mode:logical
GSM1662539 GSM1662540 GSM1662541 GSM1662542 GSM1662543
Mode:logical Mode:logical Mode:logical Mode:logical Mode:logical
GSM1662544 GSM1662545 GSM1662546 GSM1662547 GSM1662548
Mode:logical Mode:logical Mode:logical Mode:logical Mode:logical
GSM1662549 GSM1662550 GSM1662551 GSM1662552 GSM1662553
Title : Comparison of microarray platforms for measuring differential microRNA expression (Gene Expression data) [Experiment type Expression profiling by array]
summary(exprs(gse))
GSM820516 GSM820517 GSM820518 GSM820519
Min. : 137.4 Min. : 132.6 Min. : 132.6 Min. : 132.6
1st Qu.: 212.1 1st Qu.: 212.1 1st Qu.: 212.0 1st Qu.: 212.1
Median : 244.9 Median : 245.0 Median : 244.9 Median : 244.9
Mean : 1247.1 Mean : 1247.1 Mean : 1247.0 Mean : 1247.1
3rd Qu.: 508.2 3rd Qu.: 508.2 3rd Qu.: 508.0 3rd Qu.: 508.2
Max. :71775.3 Max. :71775.3 Max. :71775.3 Max. :71775.3
