Hi all, actually, I have (a) similar question(s) regarding a very non- standard Agilent data set: this is a custom 60mer oligo chip, the probes of which are designed from Arabidopsis thaliana sequence information, but intended to measure expression in the related non-model organism Arabis alpina. There are several probes per A. thaliana gene (not always the same number per gene). In addition, only the green channel has been used, so this is in effect a one-channel chip. Altogether, this is *very* similar to an Affymetrix experiment, so: is there a (simple ?) way to use the affy methods on it ? Regards Ulrike >Hi Srini, > >Not as a whole, but parts of it can apply. > >We actually use the RMA background correction method on our Agilent chips. > >The median polish section for probeset summary would not be applicable. >There are no probesets in Agilent Chips, as each probe stands on its own. > >Francois > >Srinivas Iyyer wrote: >> Dear group, >> This might be a stupid question. can I use RMA on >> Agilent data. >> srini >> >> >> ______________________________________________________________________ ______________ -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121

Hi Ulrike, You will still not be able to call the Affy probeset summarization on it, because you have different number of probes. I do not know who did the probe selection, but by default Agilent tries to select probes that give different signal as much as possible, for example relating to a splice variant or an alternative start site. This is great when you want additional insights into what the gene is doing, but rather poor if you are hoping to combine the signal together. I'm not an expert on the Affy methods, but there are likely other parts that are Affy-specific. You would have to recode a lot of the routines to deal with the different number of probe per gene and fake some kind of cdf file to inform them about the probe information. I have never heard of anyone making a convincing argument of combining Agilent probes in this way and I would strongly recommend that you try some other type of summarization. Once you have normalized your data, you can definitely perform the rest of the analysis like an Affy array. Hope this helps, Francois Ulrike Goebel wrote: > Hi all, > > actually, I have (a) similar question(s) regarding a very non- standard > Agilent data set: this is a custom 60mer oligo chip, the probes of which are > designed from Arabidopsis thaliana sequence information, but intended to > measure expression in the related non-model organism Arabis alpina. There are > several probes per A. thaliana gene (not always the same number per gene). In > addition, only the green channel has been used, so this is in effect a > one-channel chip. Altogether, this is *very* similar to an Affymetrix > experiment, so: is there a (simple ?) way to use the affy methods on it ? > > Regards > > Ulrike > >> Hi Srini, >> >> Not as a whole, but parts of it can apply. >> >> We actually use the RMA background correction method on our Agilent chips. >> >> The median polish section for probeset summary would not be applicable. >> There are no probesets in Agilent Chips, as each probe stands on its own. >> >> Francois >> >> Srinivas Iyyer wrote: >>> Dear group, >>> This might be a stupid question. can I use RMA on >>> Agilent data. >>> srini >>> >>> >>> > ____________________________________________________________________ ________________ >