Hi, I have successfully gotten external data from XLS file. Would I be able to view the array image, PM/MM data, and model-based expression indexes with this...
314
Cheng Li
l7501
Jul 2, 2003 5:14 pm
Susan, Log transformation is determined by the "Analysis/Open group/Options/Log transform expression values" option and is effective in this "Open group" ...
315
Richard Finney
rfinney5
Jul 2, 2003 6:43 pm
dChip users, you can now convert your CEL files and DAT file to popluar image formats. This is a great compliment tool for dChip and ChipInfo ...
316
gino miele (RI)
gino_miele
Jul 4, 2003 7:31 am
Hi all, I am relatively new to DCHIP and have a query that I was hoping someone might answer for me. In compare samples when I select for genes differentially...
317
Cheng Li
l7501
Jul 4, 2003 6:08 pm
Gino, This is due to the way dChip computes means by considering measurement error attached with expression values. Please see note 5/21/03 here for more ...
318
Cheng Li
l7501
Jul 4, 2003 7:47 pm
Igor, Thanks for the file. Please see below for my comments. ... different culltures (dif RNA) and done in two different times (2 wt 2 mut, with a difference...
319
sanchita_c
Jul 7, 2003 8:30 pm
Hi Dr. li, I used FDR option to look for False Discovery rate. I am geeting the following result: 1364 genes in file 'C:\Documents and...
320
Cheng Li
l7501
Jul 7, 2003 9:49 pm
Sanchita, All permutations giving large number of genes are the same comparison as the original one (1,2 vs 3,4), so you don’t need to worry about them. I...
321
st12115
Jul 8, 2003 2:50 pm
Hi, I'm trying to export some Dchip images and would like to select and color multiple sample branches. Using ctrl+click only allows me to select and color up...
322
Cheng Li
l7501
Jul 8, 2003 7:09 pm
You may check “Tools/Options/Clustering/Add new color for Control+Click”. Cheng ... From: st12115 [mailto:Sean_Tracy@...] Sent: Tuesday, July...
323
sanchita_c
Jul 9, 2003 3:43 pm
Hi Cheng, Is it possible to normalize raw data from Agilent arrays using External Data tool in dChip. Thanks, Sanchita...
324
Cheng Li
l7501
Jul 9, 2003 7:42 pm
Sanchita, You may try “Analysis/Get external data” to read in Agilent intensity values (two columns per array for the two channels): ...
325
wskamoun
Jul 10, 2003 8:46 pm
Hi, I am working on a project dealing with Affymetrix Genechip image processing. I was wondring if there is any free genechip image processing libraries...
326
Cheng Li
l7501
Jul 10, 2003 8:59 pm
Walid, DAT file is in TIFF format. See page 18 of this file: http://biosun1.harvard.edu/~cli/GATC%20software%20specifications.pdf Cheng ... From: wskamoun...
327
wskamoun
Jul 11, 2003 3:21 am
Hi, I was wondering if there is any document that describes all the image processing methodologies implmented in dChip. I mean addressing (Gridding),...
328
Cheng Li
l7501
Jul 11, 2003 5:33 am
The gridding is done in the same way as MAS (converting DAT to CEL): http://biosun1.harvard.edu/~cli/Expression%20analysis%20algorithm%20tutorial .pdf (page 6)...
329
wskamoun
Jul 11, 2003 1:57 pm
Hi, Thanks for your quick answer but I still dont find the gridding algorithm in the PDF file. They directly jump to intensity averaging assuming that the...
330
Sachin Mathur
sachinmathur79
Jul 16, 2003 4:50 pm
Hello, I'm using dchip 1.2 and having difficulty in getting the Gene Ontology annotations. I have saved them as text files. I don't have the "Tools/Make...
331
jianqings
Jul 16, 2003 5:41 pm
Hi, Does anyone know how MAS5 calculate the P/A calls. Do they report genes with absent calls some specified value or report the original intensity for those...
332
Sachin Mathur
sachinmathur79
Jul 16, 2003 7:12 pm
Hello, MAS5 bases the P/A calls on the discrimination score which is = (PM-MM)/(PM+MM). This is calculated for all the probe pairs in the probe set and is...
333
Cheng Li
l7501
Jul 16, 2003 11:21 pm
Please see Affy tech reports here: http://www.affymetrix.com/support/technical/whitepapers.affx e.g. Statistical Algorithms Description Document (pdf, 216 KB) ...
334
Cheng Li
l7501
Jul 17, 2003 12:06 am
Sachin, Some recent gene info files require V1.3: http://biosun1.harvard.edu/complab/dchip/test.htm Let me know if you observe problems in using it. Cheng ... ...
335
bleibelw2000
Jul 17, 2003 7:09 pm
Is it possible to use an excel file for microarray data that was collected on a non-affy chip? thank you...
336
Cheng Li
l7501
Jul 17, 2003 7:36 pm
You may use “Get external data”: http://biosun1.harvard.edu/complab/dchip/get%20external%20data.htm e.g. to read in cDNA array data, one may put...
337
Colin Baron
colinbaron
Jul 18, 2003 12:59 am
Has anyone seen a difference when looking at comparative analyses performed on dChip build 1.3 (March 03) vs. 1.3 (test 7-10-03)? I have conducted the same...
338
Cheng Li
l7501
Jul 18, 2003 1:21 am
Colin, This is due to the changes here (note 5/21/03): http://biosun1.harvard.edu/complab/dchip/test.htm Cheng ... From: Colin Baron...
339
nono03_2003
Jul 18, 2003 10:01 pm
Hi, I have questions about opening CEL and CDF files. I got both CEL and CDF files from one of our collaborate labs and tried to used dchip to analyze it....
340
James MacDonald
jmacdon2002
Jul 18, 2003 11:26 pm
All you need are the cel and cdf files. Are you getting some sort of error? If you say what error you get, it will be easier to figure out what the problem is....
341
jamie zhou
jzhou1688
Jul 22, 2003 3:34 pm
Hi all, Say, if I want to import a list consisting of Affymetrix ID into dChip and export the corresponding expression data or classify the imported list, is...
342
Cheng Li
l7501
Jul 22, 2003 6:27 pm
Jamie, Thanks for the suggestions. You may use “Tools/Options/Export data/Expression value” and “Tools/Classify genes”. Cheng ... From: jamie zhou...
