Bioconductor Digest, Vol 11, Issue 12I would think that ANY significant differential expression by ANOVA is evidence of presence. Also if using MAS5 or LiWong PM-MM, any significant effect including intercept would be evidence of presence but I don't think the same can be said of RMA or PM only estimates. -.- -.. .---- .--. ..-. Stephen P. Baker, MScPH , PhD(ABD) (508) 856-2625 Senior Biostatistician (775) 254-4885 fax Information Services Bioinformatics Unit Lecturer in Biostatistics , Graduate School of Biomedical Sciences University of Massachusetts Medical School 55 Lake Avenue North stephen.baker@umassmed.edu Worcester, MA 01655 USA Message: 2 Date: Fri, 09 Jan 2004 17:00:07 -0500 From: Naomi Altman <naomi@stat.psu.edu> Subject: Re: [BioC] P calls (VSN and RMA) To: w.huber@dkfz-heidelberg.de, Isaac Neuhaus <isaac.neuhaus@bms.com> Cc: rafa@jhu.edu, Petra B Ross-MacDonald <petra.rossmacdonald@bms.com>, robert.nadon@mcgill.ca, bioconductor@stat.math.ethz.ch Message-ID: <6.0.0.22.2.20040109165122.01dbfcc8@stat.psu.edu> Content-Type: text/plain; charset="us-ascii"; format=flowed I have also been working on this problem. I compared the Affy "present" calls, and calls based on various levels of normalized expression. Needless to say, these do not match well. In our study, it is known that some genes do express at very low levels in one of our conditions, and do not express under the other conditions. These genes were declared "not present" in all conditions both by Affy and by our (admittedly arbitrary) cut point (which was 50). I did a gene-by-gene ANOVA (which included all genes, even if "absent"). Interestingly enough, a few of these genes had a statistically significant ANOVA F-test and a look at the expression values confirmed that this was due to much higher expression values (2-fold or more) in the known condition. This seemed to me to indicate that perhaps we ought to consider lowering the cut point. However, if we do this, we also include a lot more genes that appear (by RT-PCR) to really be absent. So, now I wonder if I can use the ANOVA to provide information about when a gene is present. I appreciate this discussion, because it is an important issue for the group of biologists I work with. --Naomi [[alternative HTML version deleted]]

Bioconductor Digest, Vol 11, Issue 12In my previous post should have said "...any effect that is significant by ANOVA with RMA or PM only estimates would also be evidence of presence EXCEPT for intercept terms as there will always be nonspecific binding. ----- Original Message ----- From: Stephen P. Baker To: bioconductor@stat.math.ethz.ch Sent: Saturday, January 10, 2004 8:47 AM Subject: Re: Bioconductor Digest, Vol 11, Issue 12 I would think that ANY significant differential expression by ANOVA is evidence of presence. Also if using MAS5 or LiWong PM-MM, any significant effect including intercept would be evidence of presence but I don't think the same can be said of RMA or PM only estimates. -.- -.. .---- .--. ..-. Stephen P. Baker, MScPH , PhD(ABD) (508) 856-2625 Senior Biostatistician (775) 254-4885 fax Information Services Bioinformatics Unit Lecturer in Biostatistics , Graduate School of Biomedical Sciences University of Massachusetts Medical School 55 Lake Avenue North stephen.baker@umassmed.edu Worcester, MA 01655 USA [[alternative HTML version deleted]]