User: James Anderson

gravatar for James Anderson
Reputation:
820
Status:
Trusted
Location:
Last seen:
8 years, 2 months ago
Joined:
13 years, 7 months ago
Email:
j************@yahoo.com

Posts by James Anderson

<prev • 82 results • page 1 of 9 • next >
0
votes
1
answer
524
views
1
answer
question regarding RMA on 2 different U133 platforms
... Hi, I have a bunch of cel files, part of them are in U133A, others are in U133plus2. Is there a way to RMA normalize them all together by only focusing on the common probe sets? or the RMA must be one in samples from each platform and think about a way to combine them? Thanks, -James [[a ...
probe written 8.2 years ago by James Anderson820 • updated 8.2 years ago by James W. MacDonald51k
0
votes
1
answer
568
views
1
answer
question about data analysis of Genechip miRNA
... Hi, I need to analyze some Genechip miRNA data in my work, can anybody recommend some packages or methods? or everything is the same as the Affy mRNA Genechip data? Thanks, -James [[alternative HTML version deleted]] ...
mirna written 8.8 years ago by James Anderson820 • updated 8.8 years ago by Guido Hooiveld2.5k
0
votes
2
answers
500
views
2
answers
Comment: C: question regarding MAS5 normalization with reduced probes
... Hi Jim, Thanks a bunch for your help on this, it works. Sorry to bother you again, but is there a function to convert the probe indices into the probe characters you described? For example, for U133A, the probe indices is 1:247965, is there a function to convert it to Probeset1_1, ProbeSet1_2, ...ï ...
written 9.1 years ago by James Anderson820
0
votes
2
answers
500
views
2
answers
Comment: C: question regarding MAS5 normalization with reduced probes
... Hi Jim, Thanks a lot for the link. I've tried the code in the link, it works without any problem if I were to take the whole probesets out. However, I do encounter some problem when I need to take not only some probe sets, but also some probes (but not the whole probe set) out, maybe because I did ...
written 9.1 years ago by James Anderson820
0
votes
2
answers
500
views
2
answers
Comment: C: question regarding MAS5 normalization with reduced probes
... Hi Jim, Thanks for your email. I've run mas5 before, but only using default setting. From the help, it does not look like there is a way to specify which reduced set of probes you can use. In addition, from the file, it looks like it has more to do with whether the "object" is read using a reduced ...
written 9.1 years ago by James Anderson820
0
votes
2
answers
500
views
2
answers
question regarding MAS5 normalization with reduced probes
... Hi, I am trying to use MAS5 to normalize some cel files with reduced set of probes (some probes whose PM is not significantly higher than MM is filtered), does anyone know how to do this? Does that require creating a new CDF file? thanks a bunch, -James [[alternative HTML version dele ...
cdf written 9.2 years ago by James Anderson820 • updated 9.1 years ago by James W. MacDonald51k
0
votes
1
answer
720
views
1
answers
Comment: C: how to do probe set mapping between U133A and Gene 1.0 ST array
... Jim, Thanks a lot! I'll try them. -James --- On Fri, 7/9/10, James W. MacDonald wrote: From: James W. MacDonald Subject: Re: [BioC] how to do probe set mapping between U133A and Gene 1.0 ST array To: "James Anderson" Cc: "bioconductor" Date: Friday, July 9, 2010, 5:44 PM Hi James, On 7/8/2 ...
written 9.3 years ago by James Anderson820
0
votes
1
answer
720
views
1
answer
how to do probe set mapping between U133A and Gene 1.0 ST array
... Hi, I am new to Gene 1.0 ST array, could anyone give some suggestion on how to map the probe sets from U133A to Gene 1.0 ST array? Thanks, -James [[alternative HTML version deleted]] ...
probe written 9.3 years ago by James Anderson820 • updated 9.3 years ago by James W. MacDonald51k
0
votes
0
answers
269
views
0
answers
how to find out whether some Affy probe sets are Alu contaminated?
... Hi, I have a set of 200 Affymetrix probe sets as candidate biomarkers, is there a way to find out which of the 200 probe sets are Alu contaminated? Thanks, -James [[alternative HTML version deleted]] ...
probe written 9.3 years ago by James Anderson820
0
votes
1
answer
429
views
1
answers
Comment: C: question about qc function in SimpleAffy package with U95Av2 array
... Hi Vincent, I'll read more carefully about the posting guide. Below is the information I got by typing sessionInfo(), thanks. -James R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_Uni ...
written 9.4 years ago by James Anderson820

Latest awards to James Anderson

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 310 users visited in the last hour