Howdy, I'm just starting out, so forgive me if this sounds silly. I was following the example in the "textual description of affy" to normalize my data with rma and then wrote out the file. When I opened the results in excel, the column header was missing on the final column. The column header for probset name was actually the name of the first array. When I normalized using RMAexpress, I could see that the problem was that the probset name was missing and all the names of the arrays were shifted to the left. Should I simply insert the probeset column header in excel and import the file back into bioconductor to continue my analysis? I am using the most recent version of bioconductor in linux which I downloaded a few weeks ago. thanks, Ramsi This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message. Thank you. [[alternative HTML version deleted]]

What you are seeing is due to the fact that the probeset IDs are saved in the expression matrix as row names. When you export to a text file, there is no column name for the row names, so you just get an empty cell. You can automatically shift the column names over by adding col.names=NA to your write.exprs arguments. However, if you are planning to analyze your data using R or Bioconductor, you can simply avoid the whole export/import problem altogether. If you are using Bioconductor, the data is already in an exprSet, which is what almost all of the packages will expect. If you are planning to do your analysis in R without using Bioconductor, you can export to a matrix by doing something like my.data <- exprSet@exprs (you will have to substitute the actual name of your exprSet). Regards, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Haddad, Ramsi" <ramsi.haddad@vai.org> 07/11/03 10:22AM >>> Howdy, I'm just starting out, so forgive me if this sounds silly. I was following the example in the "textual description of affy" to normalize my data with rma and then wrote out the file. When I opened the results in excel, the column header was missing on the final column. The column header for probset name was actually the name of the first array. When I normalized using RMAexpress, I could see that the problem was that the probset name was missing and all the names of the arrays were shifted to the left. Should I simply insert the probeset column header in excel and import the file back into bioconductor to continue my analysis? I am using the most recent version of bioconductor in linux which I downloaded a few weeks ago. thanks, Ramsi This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

id lke to add to james' response that there is a exprs2excel funtion if you know you are going to excel. On Fri, 11 Jul 2003, Haddad, Ramsi wrote: > Howdy, > > I'm just starting out, so forgive me if this sounds silly. I was following the example in the "textual description of affy" to normalize my data with rma and then wrote out the file. When I opened the results in excel, the column header was missing on the final column. The column header for probset name was actually the name of the first array. When I normalized using RMAexpress, I could see that the problem was that the probset name was missing and all the names of the arrays were shifted to the left. Should I simply insert the probeset column header in excel and import the file back into bioconductor to continue my analysis? I am using the most recent version of bioconductor in linux which I downloaded a few weeks ago. > > thanks, > > Ramsi > > > This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message. Thank you. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >