Hi Cheng, 1) I used dChip v1.3 to export a dChip generated .CEL file. 2) I downloaded dchip_mas.exe and opened first the dChip generated .CEL file, the its...
Xitong, I'm forwarding your message to Edward J. Oakeley, the author of dchip_mas software. He may provide an updated version which handles the current CEL ...
The CEL file format has not changed with MAS5, it is still the same as with MAS4. The problem is that the new algorithm processes the file differently. This...
Oakeley, Edward
edward.oakeley@...
Dec 3, 2002 8:23 am
66
Dear all, I would be grateful for a simple explanation why I should use dChip instead of MAS 5 for my ananlysis of Affymetrix array data. Is there any...
There is a paper by Rafael Irizarry in which he compares the sensitivity and specificity of MAS5, dChip, and his Affy library using the GeneLogic spike-in...
Dan, It's ok use 4 chips to estimate phi's; however this number is too few to reliably detect probe outliers (also dChip requires > 5 chips to declare array...
I am trying to use dChip to analyze DAT files from our Affy chips. To do this dChip needs the ".cdf" file for the chips we are using (HG- U133A). We have them...
mr_magill <mzidanic@....
mzidanic@...
Dec 18, 2002 7:09 pm
70
Here is a download that contains the .cdf file you want. http://www.iobion.com/genetraffic/projectdownload/GTProject1.zip Jim James W. MacDonald UMCCC...
Dear Group, I have noticed repeatedly that dchip mixes up probe set identifiers. This was initially explained by Cheng to be a problem with cdf.bin-files that...
I'm only interested in analyzing the expression of a set of about 100 candidate genes, but I want dChip to do the normalization on the .CEL files for all the...
After normalization and model-based expression, you may use "Tools/Export data/expression value" and supply a probe set list there to get the expression values...
Reinhard, Please use the new version here (see note 12/19/02): http://biosun1.harvard.edu/complab/dchip/test.htm to correct the problem. Also I renamed...
When I analyzed gene data in dchip, I met a problem. The system gave me the error that:Celldim 712 exceeds limit. After looking at the CDF file, I wondered it...
luojingqin <luojingqi...
luojingqin@...
Dec 22, 2002 6:41 pm
77
ADMISSION NOTICE- PG Diploma in Biomedical Informatics-Distance Learning "BIOINFORMATICS INSTITUTE OF INDIA" an initiative of Confrere Educational Society (...
Hello, I have found that in the information file for the Rat UG34A chip, the entry for AA892041 (which is labeled as an EST in GenBank) was labeled as cyclic...
Jan Rodriguez
rodriguez@...
Jan 9, 2003 9:52 am
79
I think a better approach for analyzing your data is to export the MBEI and then test for differences in your samples using a t-test (or F-test if you have...
Jan, ... entry for AA892041 (which is labeled as an EST in GenBank) was labeled as cyclic nucelotide phosphodiesterase (Cam-PDE) while actually it seems to be ...
Hi, I have generated a list of genes that are differentially expressed between two animal models (with dChip expression values).Now we are going to publish it....
Christina, ... criteria? And the expression values with SE, of course. These are fine. You may mention the dChip version, the baseline array used for...
Hello, I am having difficulty using the combination of U133A+B information files. How does one combine both the HG_U133a_gene_info2 (including the protein and...
sasgharz <sasgharz@...>
sasgharz@...
Jan 14, 2003 7:47 pm
84
you need to use V1.3 to read new gene info file: http://biosun1.harvard.edu/complab/dchip/test.htm new gene info file for U133b may be created here: ...
Hi all, I think I have found a bug that is somehow involved with the export of expression data. Here is the problem. I analyzed some chips (import the chips,...
No, when I say PM/MM Data, I am referring to the icon by that name in the left panel in dChip that you can click to see the modeling information for individual...
Jim, the "Log transformation" may cause the problem. See note 12/9/02 here: http://biosun1.harvard.edu/complab/dchip/test.htm DCP files used to store log...
Cheng, I am using dChip 1.3 (a new build that you sent to me on 1/8/03) for the original analysis, and also to open the dcp file, so it should not be due to...
Jim, You are right. Please use the corrected version (you need to redo "model-based expression"): http://biosun1.harvard.edu/complab/dchip/test.htm Thank you...
Hi all Is anybody aware of a program that uses two-factor anova to analyze Affy data? The question I am trying to answer is whether any of the genes that show...
jdsandjd <josephd@...>
josephd@...
Jan 17, 2003 7:26 pm
92
Hi, Cheng: I happened to find this error in your 133A gene information file: probe set 203547_at should be CD4 antigen, and locus link is wrong too in your...
