Dear all,
I have just started to work with R and Bioconductor. Now I have a
question about
the hgu95av2probe library and also the hgu95probe library. Does
anybody know, why
not all probes are listed there.
For example the pefect match matrix in the Dilution affy batch object
from the
affycomp package is an matrix with 201800 rows (probs) but the
hgu95av2probe object only
has 199084 rows. So there is a difference of about 2700 probes. Is
their sequence unknown or
why are these probes not listed in hgu95av2probe ?
Thank you
M. Ruschhaupt
On Thu, Sep 18, 2003 at 11:37:37AM +0200, M.Ruschhaupt@dkfz-
heidelberg.de wrote:
> Dear all,
>
> I have just started to work with R and Bioconductor. Now I have a
question about
> the hgu95av2probe library and also the hgu95probe library. Does
anybody know, why
> not all probes are listed there.
These two packages are built from the "probe information files" made
public by Affymetrix (and available on the company's website).
>
> For example the pefect match matrix in the Dilution affy batch
object from the
> affycomp package is an matrix with 201800 rows (probs) but the
hgu95av2probe object only
> has 199084 rows. So there is a difference of about 2700 probes. Is
their sequence unknown or
> why are these probes not listed in hgu95av2probe ?
If you know, please share the information.
My guess (from some work I have done with that) would be that some
probes
were found to be not so good and were removed from the revised u95a
chips.
Quantifying the differences would be a cute example to show the
flexibility
of the 'affy' package... it is not a too difficult thing do
(hint: make use of the corresponding cdfenv packs).
Do not hesitate to share your code.
Hopin' it helps,
L.
>
> Thank you
> M. Ruschhaupt
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
--------------------------------------------------------------
Laurent Gautier CBS, Building 208, DTU
PhD. Student DK-2800 Lyngby,Denmark
tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
> Quantifying the differences would be a cute example to show the
> flexibility
> of the 'affy' package... it is not a too difficult thing do
> (hint: make use of the corresponding cdfenv packs).
> Do not hesitate to share your code.
>
Here is the code I used to see, which probes are not listed in the
hgu95av2probe object. It is
far away from being efficient and the difference is only checked for
the Dilution set of the
affycomp package but that should not matter.
> load("Dilution.rda")
> library(hgu95av2probe)
> p.index <-
xy2indices(hgu95av2probe$x+1,hgu95av2probe$y+1,ab=Dilution)
> length(p.index)
[1] 199084
> ind <- unlist(indexProbes(Dilution, "pm"))
> length(ind)
[1] 201800
> ind2 <- ind[! ind %in% p.index]
> length(ind2)
[1] 2716
> ind2[1:5]
1142_at1 1142_at2 1142_at3 1142_at4 1142_at5
387228 17915 239242 334935 48584
Maybe this can help to find out why these probes are not in the
hgu95av2probe object.
Markus
On Fri, Sep 19, 2003 at 09:55:25AM +0200, M.Ruschhaupt@dkfz-
heidelberg.de wrote:
>
> > Quantifying the differences would be a cute example to show the
> > flexibility
> > of the 'affy' package... it is not a too difficult thing do
> > (hint: make use of the corresponding cdfenv packs).
> > Do not hesitate to share your code.
> >
> Here is the code I used to see, which probes are not listed in the
hgu95av2probe object. It is
> far away from being efficient and the difference is only checked for
the Dilution set of the
> affycomp package but that should not matter.
>
> > load("Dilution.rda")
> > library(hgu95av2probe)
> > p.index <-
xy2indices(hgu95av2probe$x+1,hgu95av2probe$y+1,ab=Dilution)
> > length(p.index)
> [1] 199084
> > ind <- unlist(indexProbes(Dilution, "pm"))
> > length(ind)
> [1] 201800
> > ind2 <- ind[! ind %in% p.index]
> > length(ind2)
> [1] 2716
> > ind2[1:5]
> 1142_at1 1142_at2 1142_at3 1142_at4 1142_at5
> 387228 17915 239242 334935 48584
>
> Maybe this can help to find out why these probes are not in the
hgu95av2probe object.
I think one has to go to the annotation for these probes. For the
particular
example you give, the information available are:
(copy/paste from http://www.medfac.leidenuniv.nl/lgtc/db/Affy/HG-
U95A.txt)
HG-U95A 1142_at HG3432-HT3618 "Fibroblast Growth Factor Receptor
K-Sam, Alt. Splice 1" individual sequence
HG-U95A 1143_s_at HG3432-HT3620 "Fibroblast Growth Factor
Receptor K-Sam, Alt. Splice 3, K-Sam III" group members
not included
HG-U95A 1144_at HG3432-HT3621 "Fibroblast Growth Factor Receptor
K-Sam, Alt. Splice 4, K-Sam IV" individual sequence
HG-U95A 1145_g_at HG3432-HT3621 "Fibroblast Growth Factor
Receptor K-Sam, Alt. Splice 4, K-Sam IV" group members
not included
I shall be able mail a little more about alternative splicing and
Affymetrix probes within the very near future (hopefully).
L.
>
> Markus
--
--------------------------------------------------------------
Laurent Gautier CBS, Building 208, DTU
PhD. Student DK-2800 Lyngby,Denmark
tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
Growth factor are a group of cytokines, containing members like Transforming Growth Factor β-1 (TGFβ-1), Insulin-like Growth Factor I (IGF-I), Bone Morphogenic Protein 2 (BMP-2), Bone Morphogenic Protein 7 (BMP-7), and Fibroblastic Growth Factor 2 (FGF-2). TGFβ and IGF-I have been shown to stimulate the production of proteoglycans (anabolic). Additionally, IGF-I has been shown to increase chondrocyte proliferation (mitogenic). BMP-2 and BMP-7 have been shown to enhance proteoglycan synthesis, and it has been indicated that BMP-7 maybe also increase the synthesis of hyaluronic acid and its receptor CD44. FGF-2 can help the regenerative capacity of chondrocytes, as it will stimulate proliferation and redifferentiation once the chondrocytes are moved from monolayer culture to a 3D culture in a scaffold. Moreover, studies by the Loeser laboratory have shown that growth factors IGF-I and TGFβ-1 when added exogenously to the culture medium can enhance the expression of certain integrins, increasing the adhesivity of the cells to the matrix; however, TGFβ-1 had the opposite effect on the α1β1 integrin, decreasing chondrocyte affinity to collagen VI.
