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Messages 313 - 342 of 2747   Oldest  |  < Older  |  Newer >  |  Newest
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313
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...
nono03_2003
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Jul 1, 2003
11:56 pm
314
Susan, Log transformation is determined by the "Analysis/Open group/Options/Log transform expression values" option and is effective in this "Open group" ...
Cheng Li
l7501
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Jul 2, 2003
5:14 pm
315
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 ...
Richard Finney
rfinney5
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Jul 2, 2003
6:43 pm
316
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...
gino miele (RI)
gino_miele
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Jul 4, 2003
7:31 am
317
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 ...
Cheng Li
l7501
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Jul 4, 2003
6:08 pm
318
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...
Cheng Li
l7501
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Jul 4, 2003
7:47 pm
319
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...
sanchita_c
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Jul 7, 2003
8:30 pm
320
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...
Cheng Li
l7501
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Jul 7, 2003
9:49 pm
321
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...
st12115
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Jul 8, 2003
2:50 pm
322
You may check “Tools/Options/Clustering/Add new color for Control+Click”. Cheng ... From: st12115 [mailto:Sean_Tracy@...] Sent: Tuesday, July...
Cheng Li
l7501
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Jul 8, 2003
7:09 pm
323
Hi Cheng, Is it possible to normalize raw data from Agilent arrays using External Data tool in dChip. Thanks, Sanchita...
sanchita_c
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Jul 9, 2003
3:43 pm
324
Sanchita, You may try “Analysis/Get external data” to read in Agilent intensity values (two columns per array for the two channels): ...
Cheng Li
l7501
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Jul 9, 2003
7:42 pm
325
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...
wskamoun
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Jul 10, 2003
8:46 pm
326
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...
Cheng Li
l7501
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Jul 10, 2003
8:59 pm
327
Hi, I was wondering if there is any document that describes all the image processing methodologies implmented in dChip. I mean addressing (Gridding),...
wskamoun
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Jul 11, 2003
3:21 am
328
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)...
Cheng Li
l7501
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Jul 11, 2003
5:33 am
329
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...
wskamoun
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Jul 11, 2003
1:57 pm
330
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...
Sachin Mathur
sachinmathur79
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Jul 16, 2003
4:50 pm
331
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...
jianqings
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Jul 16, 2003
5:41 pm
332
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...
Sachin Mathur
sachinmathur79
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Jul 16, 2003
7:12 pm
333
Please see Affy tech reports here: http://www.affymetrix.com/support/technical/whitepapers.affx e.g. Statistical Algorithms Description Document (pdf, 216 KB) ...
Cheng Li
l7501
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Jul 16, 2003
11:21 pm
334
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 ... ...
Cheng Li
l7501
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Jul 17, 2003
12:06 am
335
Is it possible to use an excel file for microarray data that was collected on a non-affy chip? thank you...
bleibelw2000
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Jul 17, 2003
7:09 pm
336
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...
Cheng Li
l7501
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Jul 17, 2003
7:36 pm
337
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...
Colin Baron
colinbaron
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Jul 18, 2003
12:59 am
338
Colin, This is due to the changes here (note 5/21/03): http://biosun1.harvard.edu/complab/dchip/test.htm Cheng ... From: Colin Baron...
Cheng Li
l7501
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Jul 18, 2003
1:21 am
339
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....
nono03_2003
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Jul 18, 2003
10:01 pm
340
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....
James MacDonald
jmacdon2002
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Jul 18, 2003
11:26 pm
341
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...
jamie zhou
jzhou1688
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Jul 22, 2003
3:34 pm
342
Jamie, Thanks for the suggestions. You may use “Tools/Options/Export data/Expression value” and “Tools/Classify genes”. Cheng ... From: jamie zhou...
Cheng Li
l7501
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Jul 22, 2003
6:27 pm
Messages 313 - 342 of 2747   Oldest  |  < Older  |  Newer >  |  Newest
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