Hi Weiwei, Look at the $genes element from read.maimages. Hopefully it'll have what you need. Otherwise, you'll have to depend on the data provider. It's a custom chip and only they will have the annotations for it. Francois On Tue, 2007-07-17 at 19:04 -0400, Weiwei Shi wrote: > HI, Francois: > first, thanks for the detailed reply. > > The matching is done and only ~7700 probes out of ~10,100 are matched > ( and I assume they start with A_) > > However, some probeID are like > > tail(x0, 10) > [1] "A_24_P913609" "Hs345093.1" "A_23_P144999" "A_23_P399001" > [5] "A_23_P340617" "A_32_P104088" "A_32_P34372" "A_23_P62764" > [9] "Hs132898.3" "A_32_P370539" > > since it is a customized array, I think they might use UnigeneID(?), > but what's ".3"? Should it be Hs.132898? confused! > > FeatureExtractor_DesignFileName gives > D:\Array_Data\Kinder-Onko\Design Files > KinderOnko\Custom_Final_280904\012714_d_20040819.xml > > Is that right? > > Be honest, I hate people providing data w/o good annotation :( > > Kinda asking us to play the guessing game. > > Best, > > Weiwei > > > > On 7/17/07, Francois Pepin <fpepin at="" cs.mcgill.ca=""> wrote: > > Hi Weiwei, > > > > I'd assume the last one: > > > > 1st is a very old chip > > 2nd & 3rd are for CGH, not expression > > 4th is their basic human gene expression. > > > > Keep in mind that they now have 4x44 arrays that use the same non- > > control probes but has them in different positions. If the chips were > > purchased recently, they are likely the 4x44 ones, as they end up being > > a lot cheaper. > > > > The quick and dirty way of finding out: look in the feature extraction > > file, you'll see a column that says FeatureExtractor_DesignFileName in > > the header. With this should be a file that looks like > > 014868_D_F_20060807.xml. The first part (014868) says the chip type > > (design ID, actually) while the 2nd gives the annotation release date. > > Then go to http://www.chem.agilent.com/cag/bsp/array_list.asp and search > > in the list. In this case, you'd see this is the 4x44 whole genome mouse > > chip. > > > > There is a bioconductor package for the human whole genome chips: > > hgug4112a. This does not include any non-control probes, so it should > > work with both the 1x44 and 4x44. > > > > Also, the read.maimages should also grab the gene annotation that is > > included in the feature extractor software. They might be out of date, > > but it should help you to keep going. > > > > Hope this helps, > > > > Francois > > > > On Tue, 2007-07-17 at 17:43 -0400, Weiwei Shi wrote: > > > I am doing the latter now b/c I don't know the answer to the first > > > question. The data provider is sloooooowwww in reply. > > > > > > On 7/17/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > > > Weiwei Shi wrote: > > > > > Hi, there: > > > > > > > > > > I knew this is a bit off-topic but hope someone has knowledge to share: > > > > > > > > > > I found 4 zipped files about annotation from agilent: > > > > > > > > > > Human 1A(v2) > > > > > Human Genome CGH 44A > > > > > Human Genome CGH 44B > > > > > Human Genome, Whole > > > > > > > > > > I assume I can use the last one for my arrays but w/o knowing the > > > > > difference b/w them, I am not quite sure. > > > > > > > > You will need to find out what platform your arrays use or do some probe > > > > ID matching between your arrays and the annotation packages. The former > > > > is preferred. > > > > > > > > Sean > > > > > > > > > > > > > > > >