Editing
Daniel:Notebook/GenomeMiner/2013-8-6
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
=HL155= [[Daniel:Notebook/GenomeMiner|Back to Calendar]] ==MATLAB analysis== Wrote a MATLAB script to compare statistics from HL155 set. Input was a structure file of read counts for each probe. The output, shown below, is the distributions of read counts for each set. The x axis is read count, normalized to the median (1=median, 10= 10x median). The y axis is the frequency of read counts, normalized by the total number of probes. The right most bar represents the tail of the data, defined as anything greater than 10x reads over the median (basically anything with excessive numbers of reads). [[Image:Probehist HL155.png|800px]] In looking at these results, I'd say that on average 1-2% of the probes are amplified considerably over the others. Also important are the number of zero reads, summarized in the table below: {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="font-size:12pt" align="center" | align="center" width="94" height="15" | |style="font-weight:bold" width="65" | V6S1 |style="font-weight:bold" width="65" | V6S2 |style="font-weight:bold" width="65" | V6S3 |style="font-weight:bold" width="65" | V6S4 |style="font-weight:bold" width="65" | V4S1 |style="font-weight:bold" width="65" | V4S2 |style="font-weight:bold" width="65" | V4S3 |style="font-weight:bold" width="65" | V4S4 |- style="font-size:12pt" align="center" |style="font-weight:bold" height="30" | Median Read Count | align="center" | 135 | align="center" | 141 | align="center" | 115 | align="center" | 179 | align="center" | 103 | align="center" | 95 | align="center" | 200 | align="center" | 223 |- style="font-size:12pt" align="center" |style="font-weight:bold" height="30" | Number of Zero Read Probes | align="center" | 87 | align="center" | 136 | align="center" | 59 | align="center" | 9 | align="center" | 17 | align="center" | 49 | align="center" | 12 | align="center" | 1 |- style="font-size:12pt" align="center" |style="font-weight:bold" height="45" | Percentage of Zero Read Probes | align="center" | 0.5254 | align="center" | 0.8293 | align="center" | 0.4538 | align="center" | 0.0676 | align="center" | 0.5745 | align="center" | 1.3611 | align="center" | 0.2051 | align="center" | 0.0167 |} So on average, 1-2% of probes (~100-200 probes) were amplified too much per set, and around 0.5% (~50 probes) were not amplified at all.
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information