Hi, I am using version 1.6.0 of GEOquery but GDS2eSet function seems not to be working properly. It tries to use "Table", which does not exist. I replaced it for "table", but it still does not work. I am also not sure if getGEO is retrieving the information in a correct format, because I cannot access the different GSMs of the downloaded GSE file (GSE3219), even though they are present. Thank you. Luis.

On 7/19/06 10:44, "LUIS F MENEZES" <lmenezes at="" jhmi.edu=""> wrote: > Hi, > I am using version 1.6.0 of GEOquery but GDS2eSet function seems not to be > working properly. It tries to use "Table", which does not exist. I replaced it > for "table", but it still does not work. I am also not sure if getGEO is > retrieving the information in a correct format, because I cannot access the > different GSMs of the downloaded GSE file (GSE3219), even though they are > present. Luis, The function GDS2eSet works on a GDS object, not a GSE object. For GSE3219, there is no GDS, so you GDS2eSet cannot be used to make the eSet. There is an example in the vignette for GEOquery that shows some code for making an eSet from a GSE object. Hope that clarifies things a bit. Sean