Dear Bioconductor users,
Does anyone knows how to get the coordinates (x,y) for a specific
chip?
Once I know the (x,y) of a match probe, is there any formula to get
the
(x,y) of the corresponding mismatch probe?
thanks.
--------------------------------------------
Ulas Karaoz
Boston University
Ph.D.Student in Bioinformatics
zlab.bu.edu
?indexProbes
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> ulas karaoz <ulask@bu.edu> 10/31/04 7:19 PM >>>
Dear Bioconductor users,
Does anyone knows how to get the coordinates (x,y) for a specific
chip?
Once I know the (x,y) of a match probe, is there any formula to get
the
(x,y) of the corresponding mismatch probe?
thanks.
--------------------------------------------
Ulas Karaoz
Boston University
Ph.D.Student in Bioinformatics
zlab.bu.edu
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
thanks. That is not exactly what i meant, what i meant was given a
probe's coordinates from the AFFY files, i.e. HG-U133A_probe_tab, how
do I figure out the coordinates for the corresponding mismatch probe.
Is this info stored somewhere if i read the cdf file with read.cdffile
in makecdfenv package?
thanks.
On Oct 31, 2004, at 8:02 PM, James MacDonald wrote:
> ?indexProbes
>
>
>
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>>>> ulas karaoz <ulask@bu.edu> 10/31/04 7:19 PM >>>
> Dear Bioconductor users,
> Does anyone knows how to get the coordinates (x,y) for a specific
chip?
> Once I know the (x,y) of a match probe, is there any formula to get
the
> (x,y) of the corresponding mismatch probe?
> thanks.
>
> --------------------------------------------
> Ulas Karaoz
> Boston University
> Ph.D.Student in Bioinformatics
> zlab.bu.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
> not be used for urgent or sensitive issues.
>
>
>
--------------------------------------------
Ulas Karaoz
Boston University
Ph.D.Student in Bioinformatics
zlab.bu.edu
ulas karaoz wrote:
> thanks. That is not exactly what i meant, what i meant was given a
> probe's coordinates from the AFFY files, i.e. HG-U133A_probe_tab,
how do
> I figure out the coordinates for the corresponding mismatch probe.
> Is this info stored somewhere if i read the cdf file with
read.cdffile
> in makecdfenv package?
Yes it is (since the cdfenvs are build from them).
> thanks.
>
>
> On Oct 31, 2004, at 8:02 PM, James MacDonald wrote:
>
>> ?indexProbes
>>
>>
>>
>> James W. MacDonald
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
>>>>> ulas karaoz <ulask@bu.edu> 10/31/04 7:19 PM >>>
>>
>> Dear Bioconductor users,
>> Does anyone knows how to get the coordinates (x,y) for a specific
chip?
>> Once I know the (x,y) of a match probe, is there any formula to get
the
>> (x,y) of the corresponding mismatch probe?
>> thanks.
>>
>> --------------------------------------------
>> Ulas Karaoz
>> Boston University
>> Ph.D.Student in Bioinformatics
>> zlab.bu.edu
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>>
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and
should
>> not be used for urgent or sensitive issues.
>>
>>
>>
> --------------------------------------------
> Ulas Karaoz
> Boston University
> Ph.D.Student in Bioinformatics
> zlab.bu.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
ulas karaoz wrote:
> thanks. That is not exactly what i meant, what i meant was given a
> probe's coordinates from the AFFY files, i.e. HG-U133A_probe_tab,
how do
> I figure out the coordinates for the corresponding mismatch probe.
> Is this info stored somewhere if i read the cdf file with
read.cdffile
> in makecdfenv package?
> thanks.
Although indexProbes only gets you the index for a given probe, this
information can be used to get the xy coordinates and show you how
things are arranged on the chip.
> dat <- ReadAffy()
> indexProbes(dat, "pm")["1007_s_at"]
$"1007_s_at"
[1] 129340 213420 396671 82246 430968 427082 432610 72465 432865
99501 504952 443862 341432 198778
[15] 463575 10989
> indexProbes(dat, "mm")["1007_s_at"]
$"1007_s_at"
[1] 130052 214132 397383 82958 431680 427794 433322 73177 433577
100213 505664 444574 342144 199490
[15] 464287 11701
> i2xy(129340)
x y
[1,] 467 181
> i2xy(130052)
x y
[1,] 467 182
So the mm probes are located directly under the pm probes. Therefore,
the coordinates of the mm probe are x and y+1, where (x,y) are the pm
coordinates.
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
thanks for all the help, i have tried to do some comparison with the
values you have provided:
In the AFFY CDF file for U133A chip, the following line is for the
x=467, y=181:
Cell1=467 181 N control 1007_s_at 0 13
G C G 0 129339 -1 -1 99
and to x=467, y=182:
Cell2=467 182 N control 1007_s_at 0 13
G G G 0 130051 -1 -1 99
Why these indices are offset by 1 compared to yours, has this anything
to do with the package wide xy.offset = 1 option?
I am very puzzled about what are the correct indices, can I plug in
simply the indices from the CDF file, which seem to be computed as: x+
(712 * y) for U133A chip. Clearly I am missing something.
thanks.
On Nov 1, 2004, at 9:21 AM, James W. MacDonald wrote:
> ulas karaoz wrote:
>> thanks. That is not exactly what i meant, what i meant was given a
>> probe's coordinates from the AFFY files, i.e. HG-U133A_probe_tab,
how
>> do I figure out the coordinates for the corresponding mismatch
probe.
>> Is this info stored somewhere if i read the cdf file with
>> read.cdffile in makecdfenv package?
>> thanks.
>
> Although indexProbes only gets you the index for a given probe, this
> information can be used to get the xy coordinates and show you how
> things are arranged on the chip.
>
> > dat <- ReadAffy()
> > indexProbes(dat, "pm")["1007_s_at"]
> $"1007_s_at"
> [1] 129340 213420 396671 82246 430968 427082 432610 72465 432865
> 99501 504952 443862 341432 198778
> [15] 463575 10989
>
> > indexProbes(dat, "mm")["1007_s_at"]
> $"1007_s_at"
> [1] 130052 214132 397383 82958 431680 427794 433322 73177 433577
> 100213 505664 444574 342144 199490
> [15] 464287 11701
>
> > i2xy(129340)
> x y
> [1,] 467 181
> > i2xy(130052)
> x y
> [1,] 467 182
>
> So the mm probes are located directly under the pm probes.
Therefore,
> the coordinates of the mm probe are x and y+1, where (x,y) are the
pm
> coordinates.
>
> Jim
>
>
>
> --
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
>
--------------------------------------------
Ulas Karaoz
Boston University
Ph.D.Student in Bioinformatics
zlab.bu.edu
ulas karaoz wrote:
> Why these indices are offset by 1 compared to yours, has this
anything
> to do with the package wide xy.offset = 1 option?
> I am very puzzled about what are the correct indices, can I plug in
> simply the indices from the CDF file, which seem to be computed as:
x+
> (712 * y) for U133A chip. Clearly I am missing something.
> thanks.
Rafael and Laurent would know better than me, but I think the
difference
is due to different indexing between R and most other programming
languages. R indexes starting at 1, whereas most other languages start
at 0.
BTW, I get a different offset than you.
> unlist(getOption("BioC"))$affy.xy.offset
[1] 0
Best,
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
ulas karaoz wrote:
> Dear Bioconductor users,
> Does anyone knows how to get the coordinates (x,y) for a specific
chip?
> Once I know the (x,y) of a match probe, is there any formula to get
the
> (x,y) of the corresponding mismatch probe?
> thanks.
Hi Ulas,
have a look at the "probe" packages, e.g. hgu95av2probe
and the function indices2xy from affy package.
Best wishes
Wolfgang
--
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http: www.dkfz.de/abt0840/whuber
