Cheng, I'm confused. If we have a set of 4 chips, two baseline and two expermental for instance, and we run invariant gene normalization indicating the first...
Stephen, ... instance, and we run invariant gene normalization indicating the first baseline chip as the reference chip, does dChip normalize all of the chips?...
Cheng: How do you calculate the rank difference? Does the density rank means the largest difference of the densities of the probes among the probe set of a...
Dear Cheng, I would like to ask about the normalization and baseline array. I have 3 cell types, let's say: B - control cells S - a gene is knocked out E -...
Hi, We have a 4 TS and 4 IS with the probe number and the descriptions in an excel file. I got the data from the Rat UG34A chip ... i am wondering how can i...
Paul, I don't have experiences on this and am forwarding your question to dChip discussion list. You may also try MAS5 or Bioconductor normalization and...
LXu, The rank difference is computed for probe-wise, and so the invariant set is a set of probes used for determining the probe-level normalization curve. More...
I thought this should be posted: Yes. It can be read by the "Get external data" function: http://biosun1.harvard.edu/complab/dchip/get%20external%20data.htm ...
Dear Cheng, On August 1st you posted a reply to "RE: [dchip] Another question about the Normalization" (see below). I read the manual link, read the help file...
Morgen, You need to install R and R-COM: http://biosun1.harvard.edu/complab/dchip/interface_r.htm then start dChip and click the “R command” icon on the...
Dear Cheng, Validation! Yesterday, I did exactly as you describe below before I posted. Just in case the program was being capricious, I did it again this...
Morgen, The problem may be that the points are represented by circles. You may type in something like pairs(Glut4TgLiver,pch='.') to use dots to plot points....
Mirzo, Since you will compare all samples eventually, I think you better select one baseline array and normalize all arrays to it. Normalization is to adjust ...
Hi guys, I have a significantly called gene (p=0.027162 using dchip and q=1 SAM unlogged, q=4 log2) with a 6 fold change over baseline (base line mean = 306,...
Do you know how dChip defines gene as "Present" or "Absent"? I found the original flag of gene from Affymetrix raw data had been changed in dChip. Thank you!...
the determine whether it is P or A based on a discriminate score. You can get information about those analysis from affy web page. dChip recommend use affy...
Damon, Could you use this updated dchip: http://biosun1.harvard.edu/complab/dchip/dchip.1.3.exe to export the probe pattern image in all arrays of this probe...
Dear Group, We have recently loaded in some data ( CEL files). Carried out normalisation, then modelled based expression and looking at the expression values...
Hi Group, I am trying to use dChip to analyse my data. According to the manual, CEL and CDF files are needed. But from the CD that came with my REA230 chip,...
Hi, i am currently trying to export the array image with the tree after the hierachial clustering. usually my pc is comfortable with this, but i cant open...
Chris, You may try the descriptions here: http://biosun1.harvard.edu/complab/dchip/image%20view.htm#export_image For EMF files you can export the smallest...
Hi people, i am a dchip new user. I just downloaded it to my laptop and I started playing with it. What i have 20 samples (affy chips) from two different...
Sam, You can start by analyzing them as one group. More details here: http://biosun1.harvard.edu/complab/dchip/prepare%20data.htm Cheng ... From: sm1_yanas...
Hi Cheng, I am tring to install R and R com. According to the manual, I should "V1.3+] In dChip, check the "Analysis/Open group/Options/Analysis/Show `R View'...
Hi Cheng, Thank you for your reply... I have grouped all the samples in one group, ran normalization and mode-based expression. I also did the comparison...
I have found the new function to get an estimate of FDR by permutation very useful. However, I have encountered one problem. When I use two related comparison...
Xinmin, This is a good point and I will keep it in mind. For now you may check the FDR when doing a) and b) alone. If the two are close I think by doing what ...
