Edwin, For one color array, It is suggested to use MAD scaling for normalization, This feature is available in LIMMA library (R package- Linear Models for...
I would recommend the limma package. The function 'read.maimages' has a setting for reading Agilent arrays. For a useful reference I would recommend the book: ...
Dustin Potter
GENE-ARRAYS@...
Jun 26, 2008 5:31 am
19416
Hi Edwin I am not sure about a specific R package but have you tried ArrayNorm? Regards Willy Valdivia With Orion Integrated Biosciences ... Discover the...
Willy Valdivia-Granda
willy_valdivia@...
Jun 26, 2008 5:31 am
19417
Dear Edwin For the one-color agilent arrays i use the marray package. Import the gProcessedSignal as G and the gMeanSignal as R. The gProcessedSignal is...
Kristian Almstrup
GENE-ARRAYS@...
Jun 26, 2008 5:31 am
19418
Hi Edwin, we're using BioConductor packages limma and vsn for doing what you're asking for on Agilent two-color arrays and are very happy with them. I can see...
GENE-ARRAYS@...
Jun 26, 2008 5:31 am
19419
As long as you have at least two biological replicates the limma package will work. But you need at least two, because works by fitting a linear model to the...
Elliot Kleiman
kleiman@...
Jun 26, 2008 5:31 am
19420
Hi Microarrayers I am looking for Poly(dA)-DNA (Pharmacia; Cat # 27-7988-01) or polyA (Pharmacia, cat#27-7836-01) for hybridization. I checked GE website and ...
Hello all, I am trying to extract RNA from grapevine leaves. So far, RNAs are always degraded. I was wondering if anyone had any experience on this topic to...
GENE-ARRAYS@...
Jun 30, 2008 7:55 am
19422
Hi Hussein, Poly(dA) is simply an oligonucleotide. You're best off ordering it as an oligo from a company that makes oligos. Order it on a large scale (i.e. ...
Chris Seidel
seidel@...
Jul 1, 2008 8:49 am
19423
Hi Lucile, It would be helpful to know your protocol, so that people could comment on specific aspects. Does your protocol contain any reagents or steps for...
Chris Seidel
seidel@...
Jul 1, 2008 8:49 am
19424
Dear colleagues, Some time ago I have noticed a questions concerning the total number of transcripts in a single cell and transcript copies distribution within...
tanya subkhan
GENE-ARRAYS@...
Jul 1, 2008 8:49 am
19425
Dear Lucile, We are using Agilent plant RNA extraction kits and it is working great for microarray applications from a wide variety of plants and...
One-Day Intensive Microarray Data Analysis Workshop With DNA Chip Analyzer (dChip) UCLA Clinical Microarray Core is pleased to announce a one-day microarray...
We need to get rid of 3 Perkin Elmer HybArray 12 stations that are under a service agreement until 12/08 serial numbers are: 00130 00123 20285 if you know of...
haipinghao
haipinghao@...
Jul 12, 2008 5:10 am
19428
We have 3 Perkin Elmer HybArray 12 stations that are under a service agreement until 12/08 serial numbers are: 00130 00123 20285 if you know of anyone please...
Linda Almeida
lalmeida@...
Jul 12, 2008 5:10 am
19429
We're trying to design a disposable 384 well glass bottom plate that a customer can print protein microarrays in. When we print slides, they have to be washed...
Many of the researchers that use our core are running projects starting from very small samples (ie less than 50 ng to a few hundred pg). Until recently we...
Christopher Barker
GENE-ARRAYS@...
Jul 15, 2008 8:52 am
19431
... Hi Erika, I suspect you obtained that from the Genepix manual. You don't need a SNR>threshold for both channels in order to keep the spot as "good", one is...
j.delasheras@...
Jul 16, 2008 7:27 am
19432
Hi Erika, My understanding of the SNR (signal to noise ratio) filter is a way to eliminate low signal intensity spots that's hard to be differenciated from...
Ying, Jun
jun.ying@...
Jul 17, 2008 7:27 am
19433
We have successfully processed samples on Affymetrix arrays using RNA extracted from the Zymo Mini RNA isolation kits http://www.zymoresearch.com/. The...
Kristina Vartanian
vartania@...
Jul 18, 2008 7:13 am
19434
Dear All, Has anyone used Corbett CAS1200 for microarray probe preparation and would like to share their opinions on using this particular robotic system? I am...
Thanks to all who have responded on this question. We got several recommendations for the Qiagen RNeasy Micro kit and have ordered that but will also keep Zymo...
Christopher Barker
GENE-ARRAYS@...
Jul 21, 2008 7:26 am
19436
Dear all, It is now possible to perform gene expression profiling of guinea pig! We are pleased to announce that we have developed a custom gene expression...
Can anyone tell me about the NanoVue and how it compares to the NanoDrop?...
Evan
viper06_02@...
Jul 23, 2008 1:46 pm
19438
Does anyone have any experience with the NanoVue? How does it rate against the NanoDrop?...
Evan
viper06_02@...
Jul 24, 2008 7:21 am
19439
You might also compare Picodrop and NanoDrop. And NanoPhotometer and NanoVue. These are all microliter volume photometers for UV-Vis measurements, all...
Hi all, I'm trying to create an assignment for a bunch of graduate students focusing on hands-on experience with Microarrays. I am planning on using the dChip...
bwgoudey
bwgoudey@...
Jul 24, 2008 7:26 am
19441
Hi Bwgoudey, Look in GEO http://www.ncbi.nlm.nih.gov/geo/ Type in keyword e.g breast cancer AND affymetrix You will get lots of datasets which has cel files....
Evan, Both systems use small volume samples. The key differences are listed here: The NanoDrop 1000 captures and measures the absorbance of the sample between...
wanginfo
GENE-ARRAYS@...
Jul 25, 2008 7:32 am
19443
Evan, Both instruments listed only can do small volumes in a limited dynamic range and need to be recalibrated. For proteins both technologies are not able to...
