Dear All, we have recently started working with the new mouse 430 2.0 chip. The problems we still haven't managed to solve are generating a gene information...
Cheng, I read the previous posted message and downloaded the recent version of dchip, as you suggested. This solved my problem. Thanks for all efforts! Kevin...
Dear Dchip-Users! While exporting expression vallues from a filtered list, I have repeatedly experienced dchip shutting down in the middle of the process...
Kevin, Could you try not using gene info file at “Open group” and then export? Gene names may cause the problem. Can you also send me one dcp file and the...
Hi. I want to compare the focus vs. the U133 but in the MAS it is not possible to compare differend kind of chip-typs. Has anybody an idea where how to do...
I am having the exact same problem. I've used dchip v1.3 quite a bit with chips whose DAT files were labeled "HG-U133A.1sq" at the top of the file. Now I have...
Marv, See this link: http://chip.dfci.harvard.edu/biostat/cdf%20files/ Cheng ... From: fingermytuna [mailto:fingermytuna@...] Sent: Thursday, May 06,...
Hi All, Given 11-16 affy probe pairs, from the dchip, PM/MM Data, how does one find the probe sequence information?! Waiting for your reply. Thanks, Hrishi ...
Hi, I am using dChip 1.3. While performing gene clustering, the analysis log also output the sig Gene Ontology clusters. Something like: Finding significant...
Hi All, I hope i have not confused all, the problem is i have for a given gene affy 11-16 probes with their sequences, now i want to know for a given probe...
Wei, You may click the blue clustering icon on the left side for this significant cluster to see the branch and genes of this GO term highlighted in the ...
Hrishi, The ordering of probes displayed in PM/MM view of dchip is based on the CDF file and is 5' (left) to 3' (right) order. Cheng ... From: hrishikesh...
Hi, Thanks for your response. Actually, about 40% significant GO clusters (including protein domain and pathways) cannot be output. The other 60% got listed in...
Does anybody know how I can calculate my false discovery rate using dChip? This paper in J Vasc Surg. 2004 Mar;39(3):645-54 Temporal genomics of vein bypass...
Hi Crystal, Analysis -> Compare samples, Combine comparisons tab: at the bottom there is a tick box for FDR ... -- David Carter London Regional Genomics Centre...
Hi,all, Is there anybody experienced in using R command on dCHIP?I succeeded in intalling R on dCHIP but have no idea of run this function on dCHIP! I...
Hi, Its not the genes which have negative/positive values its the CALL of Affymetrix MAS 4.0 software (MAS 5.0 does not call negative values), Affymetrix...
Hi, Its not the genes which have negative/positive values its the CALL of Affymetrix MAS 4.0 software (MAS 5.0 does not call negative values), Affymetrix...
What functions do you wish to run on R? If you don't already use R, it may not be necessary to install R in order to use dchip. The built-in functions in dchip...
Both present/abscent calls and negative values are from dchip using PM/MM model. I think dchip use the same method for present/abscent calls as MAS 4.0. If...
This may be a stupid question, but when I open a group, if I check "Mask redundant probe sets," I'm told this by dChip 1.3 -- Masking out redundant probe sets...
Marv, This means that 7216 probe sets are targeting some locuslink IDs that 15061 are for. They could be for different alternative transcripts. This is only ...
Dear Dr. Li, We have used the Affy 10K chips in combination with dChip to analyze copy number alterations for a cancer cell-line. We did quadruplicates for the...
