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Larry
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@larry-57
Last seen 10.2 years ago
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Greetings Dr. Irizarry and Dr. Gautier,
I have a question regarding the affy procedures that I am hoping you
can =
help me with. I am in the process of exploring use of affy analysis
as =
an alternative to using the Affymetrix expression values and in doing
so =
I am trying to understand the process for generating expression
values. =
Specifically, the medianpolish default procedure used by the express =
function. =20
As I understand it, in calculating expression values for multiple
chips, =
medianpolish does not treat the chips independently. It runs through
=
this process of removing row and column medians for all the chips then
=
generates an overall value for all the chips with corrections for each
=
chip. The expression value generated is then calculated from these
two =
values. Does this then mean that I should expect different results =
depending on the number of chips I am analyzing?=20
For example, I've run a subset of data through the process, using
chips =
hybridized with extract from untreated cells and cells exposed to =
various treatment. I then analyzed the cells using 2 chips, 3 chips,
4 =
chips and 5 chips (ie. untreated + 1-4 treatments), and the results I
=
obtained were different each time. Below is the values generated for
10 =
genes in for the untreated condition only.
gene 2 chips 3chips 4chips 5chips=20
untreated 203307_at 8.47863 8.42976 8.213314 8.44459=20
205793_x_at 9.063024 9.022368 8.84279 9.022368=20
209168_at 7.840245 7.743475 7.584038 7.817369=20
210260_s_at 10.42869 10.37537 10.02658 10.42127=20
210373_at 8.373434 8.366322 8.076776 8.366322=20
214692_s_at 8.729106 8.765005 8.457484 8.769177=20
215294_s_at 6.884695 6.95363 6.691277 6.849249=20
216017_s_at 8.90209 8.637539 8.472341 8.830136=20
217431_x_at 7.288174 7.246028 6.960451 7.288174=20
59437_at 7.960958 8.008521 7.547648 7.834895=20
I recognize that the values don't vary greatly, but I am concerned
that =
having a treatment that causes profound effects to expression of
certain =
genes may affect my results considerably (with respect to not having
=
had done that treatment). =20
I hope my question is clear and would very much appreciate your
comments =
on this.
Regards
Larry Heisler
Dept of Laboratory Medicine and Pathobiology
Program in Proteomics and Pathobiology
University of Toronto
Toronto, Ontario Canada
l.heisler@rogers.com
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<font face="3DArial" size="3D2">Greetings Dr. Irizarry and Dr.=20
Gautier,</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">I have a question regarding the affy
=
procedures=20
that I am hoping you can help me with. I am in the process
=
of=20
exploring use of affy analysis as an alternative to using the
Affymetrix =
expression values and in doing so I am trying to understand the
process =
for=20
generating expression values. Specifically, the medianpolish default =
procedure=20
used by the express function. </font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">As I understand it, in calculating =
expression=20
values for multiple chips, medianpolish does not treat the
chips=20
independently. It runs through this process of removing row and column
=
medians=20
for all the chips then generates an overall value for all the chips
with =
corrections for each chip. The expression value generated
is=20
then calculated from these two values. Does this then mean
=
that I=20
should expect different results depending on the number of chips
I =
am=20
analyzing? </font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2"> For example, I've run a subset
of =
data=20
through the process, using chips hybridized with extract from
untreated =
cells=20
and cells exposed to various treatment. I then analyzed the
cells =
using 2=20
chips, 3 chips, 4 chips and 5 chips (ie. untreated + 1-4 treatments),
=
and the=20
results I obtained were different each time. Below is the values
=
generated=20
for 10 genes in for the untreated condition only.</font>
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<td=20 style="3D"BORDER-RIGHT:" #c0c0c0;="" border-top:="" #c0c0c0;="" border-left:="#c0c0c0;" border-bottom:="" #c0c0c0;="" background-color:="" transparent"="20" align="3Dright" x:num="3D"7.8348951315787199""><font face="3DArial=20" size="3D2">7.834895</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">I recognize that the values don't
vary =
greatly, but=20
I am concerned that having a treatment that causes profound effects
to=20
expression of certain genes may affect my results considerably =
(with=20
respect to not having had done that treatment). </font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">I hope my question is clear and would
=
very much=20
appreciate your comments on this.</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">Regards</font>
<font face="3DArial" size="3D2">Larry Heisler</font>
<font face="3DArial" size="3D2">Dept of Laboratory Medicine and=20
Pathobiology</font>
<font face="3DArial" size="3D2">Program in Proteomics and =
Pathobiology</font>
<font face="3DArial" size="3D2">University of Toronto</font>
<font face="3DArial" size="3D2">Toronto, Ontario Canada</font>
<font face="3DArial" size="3D2"><a=20 href="3D"mailto:l.heisler@rogers.com"">l.heisler@rogers.com</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2"></font>
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