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DiffTimePoint
(29 Oct 2004,
JoanZhang
)
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Susan Study
Start Date: 09 Sep 2004
Research Drive Directory: Kasper/040603/
Data Type: MassSpec
Notes:
Status:
normal: 100% complete
tumor: 100% complete
Output
Analysis Requests : 2 data sets - normal and tumor
Normal
originally it has 9 time points, the investigator combine them into 6 time points
four samples in each time points : AP VP DP LP, each sample is the average of 6 mice.
Tumor
4 time points and 3 samples (AP VP DLP—DLP is the combination of DP&LP)
Step I: based on normal find out proteins that have the following pattern
timepoint
½
3
4/5
6
10/15
40
cond
N
N
F
F
F
F
cond
N
N
N
F
F
F
cond
N
F
F
F
F
F
cond
F
N
F
F
F
F
cond
F
F
N
F
F
F
cond
F
F
N
N
N
N
cond
F
N
N
N
N
N
Totally generate 7 conds * 4 sample types (AP VP DP LP)= 28
Step II: pair wised comparison totally 6*5=30 based on normal set(data from step I result 1-5).
AP vs. VP
AP vs. DP
AP vs. LP
VP vs. DP
VP vs. LP
DP vs. LP
Step III: based on tumor set:get the pattern from step I, based on pattern 1-5, find out following patterns:
AP week10 week15
ON ON
OFF ON
ON OFF
VP week 12 week17
ON ON
OFF ON
ON OFF
DLP week10 week15
ON ON
OFF ON
ON OFF
Output
summary sheet: \KASPER\040603\deliverable
normal data set: \KASPER\040603\deliverable\normal_result
tumor data set: \KASPER\040603\deliverable\tumor_result
Change Log:
Sept. 22th: change timepoint of cloumn AK from 1 week to 12 weeks
Sept. 22th: delete 3 samples of 18 weeks in tumor data set.
Oct. 4th: change column AK type VP back into week 1.
Oct. 22th: change question #1 and #3 in tumor set (change week18 to week15)
Contact Info:
Primary Study Contact Person: Susan Kasper
Analysts
NimishGautam
JoanZhang
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Topic revision: r5 - 29 Oct 2004,
JoanZhang
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