Dear list,
I'm trying to obtain a list of mouse homologs of human genes present
in
Affymetrix chips (human hgu133plus2 and mouse 430) following the
homology
packages Vignette, but I didn't succeded. Here is the code and the
error
messages I got.
I'm using R-2.1.1 and Bioconductor 1.6 package.
Could you help me?
Thanks, Roberta
>library("mmuhomology")
>subset(mmuhomologyORGCODE, species_name == "Homo sapiens")
Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo
sapiens") :
Object "species_name" not found
>temp <- mget(mmuhomologyHGID, mmuhomologyDATA)
>tempFun <- function(x) {
for (i in x) {
if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
"hsa" && i[["homoPS"]] > 90) {
return(i)
}
}
return(NA)
}
>goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp,
tempFun)
Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" &&
i[["homoPS"]] > :
missing value where TRUE/FALSE needed
**********************************************************************
********
DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information
contai...{{dropped}}
Bosotti, Roberta [Nervianoms] wrote:
> Dear list,
>
> I'm trying to obtain a list of mouse homologs of human genes present
in
> Affymetrix chips (human hgu133plus2 and mouse 430) following the
homology
> packages Vignette, but I didn't succeded. Here is the code and the
error
> messages I got.
> I'm using R-2.1.1 and Bioconductor 1.6 package.
> Could you help me?
> Thanks, Roberta
>
>
>>library("mmuhomology")
>>subset(mmuhomologyORGCODE, species_name == "Homo sapiens")
>
> Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo
sapiens") :
>
> Object "species_name" not found
What version of the mmuhomology package are you using? This works for
me.
> subset(mmuhomologyORGCODE, species_name =="Homo sapiens")
species_name tax_id tla
24 Homo sapiens 9606 hsa
>
>>temp <- mget(mmuhomologyHGID, mmuhomologyDATA)
>>tempFun <- function(x) {
>
> for (i in x) {
> if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
> "hsa" && i[["homoPS"]] > 90) {
> return(i)
> }
> }
> return(NA)
> }
>
I think you are missing something here. You also have to test for
homoType == "B". If homoType == "c", then you will return an NA, which
is why your tempFun is erroring out.
tempFun <- function(x) {
for (i in x) {
if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
"hsa" && i[["homoType"]] == "B" && i[["homoPS"]] > 90) {
return(i)
}
}
return(NA)
}
HTH,
Jim
>>goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp,
tempFun)
>
> Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" &&
> i[["homoPS"]] > :
> missing value where TRUE/FALSE needed
>
>
>
>
> ********************************************************************
**********
> DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information
contai...{{dropped}}
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Dear Jim,
thanks for your help, it's working now.
I have a further question, once I got the HomologeneIDs, I'd like to
get the
Accession numbers for both human and mouse.
The HomologeneIDs that I find do not match with the ones I can
retrieve from
the NCBI Homologene home page, possibly because they are based on two
different release. Do you know where I could find HomoloGene and
LocusLink
database release that where used in the package?
Thanks again for your kind support,
Roberta
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon@med.umich.edu]
Sent: Monday, July 04, 2005 2:07 PM
To: Bosotti, Roberta [Nervianoms]
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Problems with homology packages
Bosotti, Roberta [Nervianoms] wrote:
> Dear list,
>
> I'm trying to obtain a list of mouse homologs of human genes present
in
> Affymetrix chips (human hgu133plus2 and mouse 430) following the
homology
> packages Vignette, but I didn't succeded. Here is the code and the
error
> messages I got.
> I'm using R-2.1.1 and Bioconductor 1.6 package.
> Could you help me?
> Thanks, Roberta
>
>
>>library("mmuhomology")
>>subset(mmuhomologyORGCODE, species_name == "Homo sapiens")
>
> Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo
sapiens")
:
>
> Object "species_name" not found
What version of the mmuhomology package are you using? This works for
me.
> subset(mmuhomologyORGCODE, species_name =="Homo sapiens")
species_name tax_id tla
24 Homo sapiens 9606 hsa
>
>>temp <- mget(mmuhomologyHGID, mmuhomologyDATA)
>>tempFun <- function(x) {
>
> for (i in x) {
> if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
> "hsa" && i[["homoPS"]] > 90) {
> return(i)
> }
> }
> return(NA)
> }
>
I think you are missing something here. You also have to test for
homoType == "B". If homoType == "c", then you will return an NA, which
is why your tempFun is erroring out.
tempFun <- function(x) {
for (i in x) {
if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
"hsa" && i[["homoType"]] == "B" && i[["homoPS"]] > 90) {
return(i)
}
}
return(NA)
}
HTH,
Jim
>>goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp,
tempFun)
>
> Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" &&
> i[["homoPS"]] > :
> missing value where TRUE/FALSE needed
>
>
>
>
>
**********************************************************************
******
**
> DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information
contai...{{dropped}}
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be
used for urgent or sensitive issues.
**********************************************************************
********
DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information
contai...{{dropped}}
Bosotti, Roberta [Nervianoms] wrote:
> Dear Jim,
>
> thanks for your help, it's working now.
> I have a further question, once I got the HomologeneIDs, I'd like to
get the
> Accession numbers for both human and mouse.
> The HomologeneIDs that I find do not match with the ones I can
retrieve from
> the NCBI Homologene home page, possibly because they are based on
two
> different release. Do you know where I could find HomoloGene and
LocusLink
> database release that where used in the package?
For the HomoloGene release, see ?mmuhomology. I'm not sure if this was
built using LL or Entrez Gene ids. Since it was built on 15 May, I
think
Entrez Gene ids would have been used, but the URL for HomoloGene in
?mmuhomology points to an old build that seems to use LL ids. Maybe
Seth
Falcon or Chenwei Lin can comment?
Best,
Jim
>
> Thanks again for your kind support,
>
> Roberta
>
--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Hi Roberta,
On 4 Jul 2005, jmacdon at med.umich.edu wrote:
>> thanks for your help, it's working now. I have a further question,
>> once I got the HomologeneIDs, I'd like to get the Accession numbers
>> for both human and mouse. The HomologeneIDs that I find do not
>> match with the ones I can retrieve from the NCBI Homologene home
>> page, possibly because they are based on two different release. Do
>> you know where I could find HomoloGene and LocusLink database
>> release that where used in the package?
>
> For the HomoloGene release, see ?mmuhomology. I'm not sure if this
> was built using LL or Entrez Gene ids. Since it was built on 15 May,
> I think Entrez Gene ids would have been used, but the URL for
> HomoloGene in ?mmuhomology points to an old build that seems to use
> LL ids. Maybe Seth Falcon or Chenwei Lin can comment?
The homologene data provided by NCBI underwent a significant change
prior to the BioC 1.6 release. As part of the change, the homology
data for a number of species that were previously included in the data
were removed. The meaning of the homologene IDs also changed, I
believe.
For this release we decided it was best to stick with the homology
packages from the previous release --- they were rebuilt for
compatibility with R 2.1.x, but if I am remembering the events
correctly, the data in the homology packages is identical to what was
available in the 1.5 release.
Our team _is_ working on an updated set of homology packages that will
be made available in the development annotation repository soon.
Hope that helps explain what you are seeing.
Best,
+ seth
Hi Seth
Yes, it make sense. Thanks for the explanation.
Regards, Roberta
----------------------------------------------------------------------
Hi Roberta,
On 4 Jul 2005, jmacdon at med.umich.edu wrote:
>> thanks for your help, it's working now. I have a further question,
>> once I got the HomologeneIDs, I'd like to get the Accession numbers
>> for both human and mouse. The HomologeneIDs that I find do not
>> match with the ones I can retrieve from the NCBI Homologene home
>> page, possibly because they are based on two different release. Do
>> you know where I could find HomoloGene and LocusLink database
>> release that where used in the package?
>
> For the HomoloGene release, see ?mmuhomology. I'm not sure if this
> was built using LL or Entrez Gene ids. Since it was built on 15 May,
> I think Entrez Gene ids would have been used, but the URL for
> HomoloGene in ?mmuhomology points to an old build that seems to use
> LL ids. Maybe Seth Falcon or Chenwei Lin can comment?
The homologene data provided by NCBI underwent a significant change
prior to the BioC 1.6 release. As part of the change, the homology
data for a number of species that were previously included in the data
were removed. The meaning of the homologene IDs also changed, I
believe.
For this release we decided it was best to stick with the homology
packages from the previous release --- they were rebuilt for
compatibility with R 2.1.x, but if I am remembering the events
correctly, the data in the homology packages is identical to what was
available in the 1.5 release.
Our team _is_ working on an updated set of homology packages that will
be made available in the development annotation repository soon.
Hope that helps explain what you are seeing.
Best,
+ seth
**********************************************************************
********
DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information
contai...{{dropped}}