Thank you Jim for kindly answering my questions! Very much appreciated!! James W. MacDonald wrote: > Hi Xingmei Wang, > > Xingmei Wang wrote: >> Hi all, >> I have problems analyzing affymetrix data and would like to seek help >> from the list. >> 1. I tried to create the design file by copying the design table from >> abf1 data. In Windows version R2.8.0, the data name is "abf1", while >> in Unix R2.8.0, the data name is "abf1.raw". Why? > > I assume because you named it that way. R doesn't append different > things to variable names randomly (or based on the OS). *I didn't name abf1 data. It's a data coming with package "maanova". I assumed people on this list have experience using this data. :-P * > >> >> 2. I saw probeID for abf1 data has the following format: >> "1415670_at" "1415671_at" "1415672_at" "1415673_at" >> "1415674_a_at". But the probe IDs I obtained from my data look like >> this: >> "7892501" "7892502" "7892503" "7892504" "7892505" "7892506" "7892507" >> "7892508" "7892509" "7892510" >> Is there something wrong with my data? > > Well, the probe IDs for abf1 appear to come from the Mouse430_2 chip, > and your data appear to be from either a Human Exon ST or Gene ST > chip. So it depends on what exactly you mean by 'wrong'. *Thanks for this answer! My data did come from a Human Exon ST chip* > > I think you need to think a bit more about what you are doing and what > you expect, and perhaps then you will be able to formulate a question > that can be answered by someone on this list. Right now it isn't clear > to me what you have done, nor is it clear what you expect, so it is > impossible to help clear up any misunderstanding you may be having. > *Sorry if I didn't make my questions clear! I indeed don't have much experience on genetics data, so it's hard to formulate a question. I'll try to do more research on the archives next time.* > Also, please read the posting guide: > > http://www.bioconductor.org/docs/postingGuide.html > > Asking the right question in a reasonable manner is not that > difficult, but it does take some work on your part, and the likelihood > of getting answered is often directly proportional to how well you ask > the question in the first place. *Totally agree!!* > > Best, > > Jim > > > >> >> Thanks! >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Xingmei wang , MS Biostatistician Biostatistics Analysis Center (BAC) University of Pennsylvania School of Medicine Center for Clinical Epidemiology and Biostatistics 519 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104 Phone: 215-898-1560 Fax: 215-573-1203 Email: xwang5 at mail.med.upenn.edu Website: http://www.cceb.med.upenn.edu/services/bac/