User: David A.

gravatar for David A.
David A.70
Reputation:
70
Status:
New User
Location:
Last seen:
5 years, 2 months ago
Joined:
8 years, 9 months ago
Email:
d*******@hotmail.com

Posts by David A.

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
503
views
1
answer
affymetrix rat 2.0 gene annotation issue
... Dear users, in case it is of help to anyone, just for the records or if someone can share some comments... I have searched in the list for similar issue but have not found anything related. We have just performed a Rat 2.0 Gene experiment and have found that current Affymetrix annotation files (ve ...
annotation written 5.2 years ago by David A.70 • updated 5.2 years ago by Marc Carlson7.2k
0
votes
1
answer
425
views
1
answer
Different probesets but same expression values?
... Dear list, I have just performed an analysis on a set of hugene2.1 arrays. I have normalised them using RMA method and have done statistical analysis using limma. I found that probesets for same gene have exactly the same expression values and I wonder if anyone can explain. Here one example. Val ...
limma written 5.7 years ago by David A.70 • updated 5.7 years ago by James W. MacDonald51k
0
votes
2
answers
2.0k
views
2
answers
Comment: C: creating GRanges and reading BAM files
... Dear Michael and Hervé, thanks ever so much for your help. I also found this link http://davetang.org/wiki/tiki-index.php?page=SAM that states that just removing the P operation directly from the alignment will suffice to convert to unpadded format, as you also say. So I transformed form BAM to ...
written 7.6 years ago by David A.70
0
votes
2
answers
2.0k
views
2
answers
Comment: C: creating GRanges and reading BAM files
... Thanks a lot Michael. I will modify my pseudo-bed file accordingly. Regarding padding not being supported, and while waiting to see if it ever gets support so that I can continue with analysis, is there any tool that will automatically unpad the alignment? or do people create their own scripts to ...
written 7.6 years ago by David A.70
0
votes
2
answers
2.0k
views
2
answers
creating GRanges and reading BAM files
... Hi list, sorry for a simple question, but I am a newbie a bit lost reading all the information on how to handle NGS data using R tools. I have a set of BAM files from Junior sequencer, one BAM per amplicon per sample (Roche's software does not output one single BAM file per sample including all am ...
coverage convert written 7.6 years ago by David A.70 • updated 7.6 years ago by Sunny Yu Liu80
0
votes
0
answers
232
views
0
answers
odd limma results
... Hi Jim, thanks a lot, that makes perfect sense! big mistake! results make more sense now. Best, D [[alternative HTML version deleted]] ...
written 8.8 years ago by David A.70
0
votes
1
answer
680
views
1
answer
odd limma results?
... Hi list, I have a one-color setup with 238 samples and 6 conditions, for a geneset of just over 400 probes (targeted array). One of the conditions is control and the rest are experimental conditions. After normalization using vsn I would like to make a comparison first between the control and the ...
vsn limma written 8.8 years ago by David A.70 • updated 8.8 years ago by James W. MacDonald51k

Latest awards to David A.

Popular Question 5.2 years ago, created a question with more than 1,000 views. For creating GRanges and reading BAM files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 177 users visited in the last hour