... These are the PSI of one gene, 16 probes in a set, using PM only model in Dchip. I thought the sum of square of PSI should be the same number of probe(16)....
... iteration ? Yes. This phi is a probe outlier since it has large value (phi^2 > sum(phi^2) * 0.9) and probably it also the large standard error attached....
... numerical-statistical evaluation (normalization, evaluation of mean/median/sd, fitting, clustering)? Outlier expression value refers to the "array outlier"...
... cut it out from the saved jpeg image? In V1.2, you may use Shift+Left key in the clustering picture to zoom away the Function column; or you may delete...
Hi, I forgot about this. Does dChip generate its own A/P calls or just use those from Affy MASS? If yes, how similar they are? ... Do you Yahoo!? U2 on...
I think it's better to supply dChip with Affy TXT files containing A/P calls; otherwise dChip uses a simplified version of MAS4 algorithm to make calls. More...
Sophie, Thanks for sharing your experiences. How many samples do you have for each sample group? dChip "Compare samples" menu provides several gene-wise...
Dear Dr. Li, In order to normalize MAS5 signal values in dCHIP, should I use the scaled signal values or non-scaled signal values. Xuewen...
xuewensong
xuewensong@...
Nov 14, 2002 8:13 pm
37
Hi, I have just started using dchip for our Affy data. I was wondering would it be possible to get the list of the genes which are invariant when dchip looks...
sanchita_c
sanchita_c@...
Nov 14, 2002 8:14 pm
38
Hi, Dr. Li and colleagues: I started to use Dchip for our data analysis a few months ago and I should say it is really a nice software. Now some questions have...
Did you read in MAS5 values by "Analysis/Get external data" or by "Analysis/Open group" with "Read in MAS5 Signal" checked? In the first case it does not...
Jeff, ... depend? If you have fewer samples, the chance of the model to pick up probe and single outliers, as well as array outliers is smaller. As a result...
Currently this is not feasible in dChip. One problem is that if you read in CEL files, the normalization is performed at the PM/MM probe level; so one or more...
Dear Dr. Li, I am having some problems regarding Baseline array. I have three replicate arrays for untreated sample and three replicates for treated. When I...
sanchita_c
sanchita_c@...
Nov 15, 2002 8:01 pm
43
... untreated replicates and similarly one of the treated array as base line for the treated arrays or only one of the array as base line for treated as well ...
Hi All, I think there is a bug in 1.2. When I compared some samples and output the data into an Excel spreadsheet, the gene name, accession number, ...
could you check to make sure that the "gene information file" is correctly read in at the "Analysis/Open group" step? You may email me the dchip output ...
Thanks Cheng, I overlooked that part... James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 ...
Hi, all I am trying to normalize MAS 5 Signals at expression index level. And I just wondered how many red dots ( invariant probe sets ) are selected by dChip...
seogweonkong
skong@...
Nov 20, 2002 9:03 pm
49
the method is similar to what's described here: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm#isn but applies to the expression value...
Dear Cheng Thank you very much for the informations. ... When fitting the running median curve at the two ends, 5% of the ˇ°invariantˇ± points are used to...
seogweonkong
skong@...
Nov 20, 2002 9:55 pm
51
... cubic B spline is used for curve fitting? In dChip a running median curve is fitted to the invariant set as the normalization curve. 5% of the invariant...
Dear Cheng Affy's HG-U133 set has 100 genes as a sort of invariant set, and they use these for robust normalization. Is 100 too small in number compare to 5%...
seogweonkong
skong@...
Nov 20, 2002 10:46 pm
53
For dChip’s running media curve fitting to work well, the invariant set should have > 600 genes or probes to determine a normalization curve covering the...
Cheng, I'd like to inquire about the possibility to use/plug-in quantile normalization in dChip instead of invariant set. The question has a very practical...
Nik, thanks for letting me know this. Here is affy annotation of this probe set: Consensus includes gb:AL022398 /DEF=Homo sapiens DNA sequence from PAC 434O14...
... I'll look in to it a bit and let you know. Thanks for the clarification. Nik...
nik
nik@...
Nov 26, 2002 1:21 am
57
Cheng and all: There are probably a very small number that aren't mapping perfectly in the dchip gene info files. For the moment, if one has a gene of...
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