On 2016 Nov 21, ATUL BUTTE commented:

Wow, sorry for the delay in replying! Yes, you are correct. The correct data set is GDS1615. Apologies for this error.

On 2016 May 03, Gregory Stupp commented:

It seems the authors have referred to the wrong GEO data set (GDS2642: colonoscopic biopsies from CD or UC patients), when the data in fact looks to have come from GDS1615: peripheral blood mononuclear cells from CD or UC patients).

As an example. The gene with the highest fold change in Table S1 is SERPINB2. This fold change can be seen in the GEO profile graph for GDS1615: http://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS1615:204614_at but not from GDS2642: http://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS2642:37185_at

I verified the rest of the genes using the data from the SOFT files and also using geo2r: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE3365 https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE6731

On 2016 May 03, Gregory Stupp commented:

It seems the authors have referred to the wrong GEO data set (GDS2642: colonoscopic biopsies from CD or UC patients), when the data in fact looks to have come from GDS1615: peripheral blood mononuclear cells from CD or UC patients).

As an example. The gene with the highest fold change in Table S1 is SERPINB2. This fold change can be seen in the GEO profile graph for GDS1615: http://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS1615:204614_at but not from GDS2642: http://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS2642:37185_at

I verified the rest of the genes using the data from the SOFT files and also using geo2r: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE3365 https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE6731