I downloaded a microarray from the GEO database. The platform is GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. I used a package from Bioconductor to transform the prob id to Ensembl id. After that, I downloaded the lncRNA annotation from GENCODE, the latest release and found out all of the Ensembl ids of lncRNA. What I want to do is get all of the lncRNA from the probe set. But the result is only 500 or so. A paper used the same microarray and got about 5000 lncRNA. Is there anything wrong with me? Or who can give me some advice about how to get the lncRNA from a probe set. I also want to get the lncRNA from TCGA dataset. Thanks in advance!