Dear Dr. Li: I downloaded dChipsnp from http://www.biostat.harvard.edu/complab/dchip/snp/ and try to use it look at 100k array data. I downloaded the library...
Hi, I'm having trouble making the genome info file for the 50K Xba array. I have tried following the instructions in the dChip manual but I don't get where I...
I'm trying to combine the two sub-arrays of 120K data: Xba set and Hind set. Following the instructions in the dChip manual, I obtain signal values using "Open...
I have never use this function, let me check it out. ... ____________________________________________________ Start your day with Yahoo! - make it your home...
Hi everyone Does anyone have a gene information file for hu133 plus 2? Please email me direct! Thanks Lawrence [Non-text portions of this message have been...
Hello! I used "get external data" to read in GCOS signal and P/A call. I am a bit confused about where the S.E. are calculated from when I compare samples. I...
Hi Moon, It is a big file. More than 20 MB. I cant send it across mail. If you have an ftp place let me know. I will place it there Thanks and Regards Jai...
Yes the SE are 0 for external data. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On Behalf Of oat243 Sent: Thursday, August 04, 2005...
Brian, You can use the info files here: http://biosun1.harvard.edu/complab/dchip/snp.htm Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com]On...
dear all, i would like to use dChip to analyze my codelink uniset 20K (human) microarray. The chip image was processed with the Codelink expression 4.1...
Thanks - Cheng has sorted me out though. Best Lawrence _____ From: Jai Prakash Mehta [mailto:jai.mehta2@...] Sent: Thursday, August 04, 2005 8:28 AM ...
Hi all, This is regarding paired t-test option in dchip Analysis==>Compare Samples. My question is how the system recognizes which two chips form a pair. The...
Hello all, I am new user of this dChip program and analysing my C elegans affymetrix arrays. When I try to import affy cel files (version 3) into dChip through...
Hello All, So this is my second query about dChip within an hour. Sorry about that. 1. User manual suggests that there is no need of normalization if median ...
Hi Prasad, Thats not a thing of concern, but if you provide the output of MAS software, it will take the calls from that file, otherwise it calculates on its...
Jai, "paired t-test" assumes the first baseline sample to be compared with the first experiment sample, and so on. If the samples are paired, it's better to...
Hello All, Wondered if there is any avid user of dChip here who can answer my yesterday's query. After working a bit today, I came up with few more queries. 1....
Hello All, Wondered if there is any avid user of dChip here who can answer my yesterday's query. After working a bit today, I came up with few more queries. 1....
Prasad, 1. It's probe intensity value. 2. "Analysis/Save log" is the way to save messages. You can get the file names of the data file saved from the log. ...
Dear all: I am a beginning user of dchip package and trying to run on it to re-produce the supplementary figure 1 in paper Integrative genomic analyses...
You should use Affy Early access CDF file (the first two files here): http://chip.dfci.harvard.edu/biostat/cdf%20files/ 100K and 120K mean the same. Cheng ... ...
Hi, I am recently carried out some microarray analysis using 1.2 fold change as one of my comparison criteria. This gave me a reasonable working list approx...
i have carried out an affymetrix experiment using three biological replicates (the most we could afford). the experiment is looking at cell line response to...
Hello members, I am getting the following error when using the Analysis\Chromosome feature: Chromosome 1 length exceeds that of cytoband; are they from the...
David, What arrays are you working with? Make sure the genome info file and cytoband file are based the same UCSC genome assembly. Otherwise genes and SNPs (if...
This paper has a good example of using 3 replicates to find the gene candidate: Chemokine receptor CXCR4 downregulated by von Hippel-Lindau tumour suppressor...
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