Hi everyone, I have a big problem with my microarrays, and it has been driving me nuts for almost a year and a half... My problem is that when I hybridize, the...
Hi Igor, It sounds to me as if you had a slight non-specific background signal on the non-spotted surface with Cy5 which either does not happen with Cy3 or...
Hi. We've experimented the same problem some times ago performing hybridizations with oligo slides. In fact our results showed a lot of down-regulated genes...
Dear Igor: The "traditional: answer when a DNA spots show lower background than the surrounding slide is the slide blocking protocol needs improvement, dye ...
Hi Igor, Do you really expect signals at 50~100 while the controls were saturated? Are these low expressors? It seems beside high background issue, your...
Hello everyone, We need guidence from researchers who have been working on geneSpring/Arrayassist or Affymetrix - clustering K mean clustering - ANOVA...
The answer below is not accurate. We have an Axon 4000B. I know that the manufacturer says you can change the PMT levels between slides in one experiment,...
maggie
maggieww@...
Jun 11, 2007 6:09 am
19006
Periodic calibration of the scanner is needed. Another option, we printed a pre-scan mini array on the top of the target array for justification of PMT. It...
Liu, ZLewis
ZLewis.Liu@...
Jun 11, 2007 6:10 am
19007
... I have used a number of scanners, but right now I just use a GenePix 4200L. Changing PMT settings shouldn't alter the final results very much, and that's...
j.delasheras@...
Jun 11, 2007 6:10 am
19008
Hi Igor, The inverse spot phenomenon you reported can be suppressed either by an improved blocking procedure as Todd suggested, or by using negatively charged...
Dear all, We are working with low density short oligonucleotide arrays (for microbial diagnostics), hybridised with a single colour (Cy3). Signals are...
Hi all, I have read some papers mentioned how they use Affymatrix microarray chip to measure the 5'/3' ratio of GAPDH as an indication for RNA integrity. Does...
Hi Bala, I think that referencing the manual would be fine. It should though the ratio of both GAPDH and b-actin. Agnes ... -- Dr. Agnieszka Lichanska (PhD) ...
Agnieszka Lichanska
a.lichanska@...
Jun 12, 2007 5:14 am
19012
... I think you will find this is a common enough metric not to require referencing. There is no explicit reference for example in this paper: ...
I've been using the 4200AL and have noticed the same thing. I'm wondering if it is a general property of scanners that utilize a PMT, or if it is scanner...
I will not say your findings are wrong, however I find it very hard to believe that after processing and normalisation you will have any significant...
j.delasheras@...
Jun 12, 2007 7:56 pm
19015
Somebody could give me some advice about the softwares which fit to analyze the Nimblegen microarray data. Thanks!...
Dear Gene Arrays Discussion list, we did not write up a paper about this work, however, we have now found the data from 2004 and, in fact, using the Axon 4000B...
maggie
maggieww@...
Jun 13, 2007 8:05 pm
19017
... You could try NMPP: http://plantgenomics.biology.yale.edu/nmpp/ If you're familiar with BioConductor then the 'oligo' package (and other oligo array...
I've been using PAXgene System since 2004. After Peripheral Blood Total RNA extraction, I follow a labeling protocol similar to that of Affymetrix to obtain...
vir.riojanita
vir.riojanita@...
Jun 14, 2007 6:26 pm
19019
I've been using PAXgene System since 2004. After Peripheral Blood Total RNA extraction, I follow a labeling protocol similar to that of Affymetrix to obtain...
vir.riojanita
vir.riojanita@...
Jun 14, 2007 6:28 pm
19020
In my understanding this is really clear when two-colour hybridisations are scanned and analysed. I am not so sure about one-colour arrays? Kind regards, Lev ...
You might want to check some recent papers that have data on this issue (e.g., Shi L, Tong W, Su Z, Han T, Han J, Puri RK, Fang H, Frueh FW, Goodsaid FM, Guo...
Fuscoe, James
james.fuscoe@...
Jun 15, 2007 7:49 pm
19022
EMERALD (Empowering the Microarray-Based European Research Area to Take a Lead in Development and Exploitation) is a project to establish and disseminate...
Dear list I'm in the process of reporting my array results, and have been using DAVID to assign functions to my gene list. My genes are assigned to enriched...
Hi Kirsteb, I use Genmapp for that. And I prefer putting my results as table rather than any type of pie chart as pie chart is at-times misleading. Commonly,...
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