[BioMart Users] link probes to exons

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[BioMart Users] link probes to exons

Talloen, Willem [JRDBE]

Hi all,

 

I would like to link probes to exons as defined in Ensemble. The problem I face is that I cannot find probe IDs in Ensemble mapping.

Could anyone help me with this? Probably biomaRt is a logical approach, but I cannot find it. I’m using alternative cdf from Brainarray.

 

I tried via xy coordinates (see below), but there is quite some redundancy and it is not comprehensive…

 

To make it more specific, below chunks of code that I’m currently using.

 

Thanks in advance!

Willem

 

 

# create probe intensity matrix for each probeset

for (i in 1:length(gNames)) {

      myProbeSet <- gNames[i]

      myPmindex <- unlist(pmindex(dataPreprocessed, myProbeSet))

      myDat <- intensity(dataPreprocessed)[myPmindex, ]

                  main = fProbeSet)

}

> head(myDat[,1:5])

        2720.CEL  2724.CEL  2725.CEL  2727.CEL  2728.CEL

442478 2335.2318  943.1485 2239.6485 2250.0652 2247.3568

975758 2695.0235 1232.8152 2923.0652 2794.6485 2889.9402

211794  924.3985  383.6485  856.5652  942.0652  803.8152

388714 1377.1485  764.0652 1404.8568 1622.5652 1447.1485

137675 4211.3152 2051.3985 4294.8985 4459.4818 3699.2318

985031 3602.1485 1634.2318 3607.2735 3501.6068 3442.6485

 

 

 

# load exon information

ensMap <- read.delim('../Mouse4302_Mm_ENSE_mapping.txt', sep = '\t')

> head(ensMap)

         Probe.Set.Name Chr Chr.Strand Chr.From Probe.X Probe.Y

1 ENSMUSE00000097912_at  10          -  6791726     451     421

2 ENSMUSE00000097912_at  10          -  6791765     724     625

3 ENSMUSE00000097912_at  10          -  6791790     613     565

4 ENSMUSE00000097912_at  10          -  6791850     147     367

5 ENSMUSE00000097912_at  10          -  6791866     790     251

6 ENSMUSE00000097912_at  10          -  6791883     405     115

  Affy.Probe.Set.Name

1          1451547_at

2          1451547_at

3          1451547_at

4          1451547_at

5          1451547_at

6          1451547_at

 

# link via xy coordinates

coord <- paste(ensMap$Probe.X, ensMap$Probe.Y, sep = '.')

 

> i2xy(as.numeric(rownames(myDat)))

        x   y

[1,] 595 441

[2,] 811 973

[3,] 371 211

[4,] 939 387

Willem Talloen

Janssen Pharmaceutica

Biostatistics and Programming GDO CoE

Turnhoutseweg 30, box 270

2340 Beerse 1

Belgium

Phone +32(0)14603434       Fax +32(0)14605802

[hidden email]

 

Janssen_Hor_RGB

 


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Re: [BioMart Users] link probes to exons

Arek Kasprzyk
Hi Willen,
you need a biomaRt specialist Steffen here (cc'ed on this email)

a

On Thu, Nov 10, 2011 at 6:45 AM, Talloen, Willem [JRDBE] <[hidden email]> wrote:

Hi all,

 

I would like to link probes to exons as defined in Ensemble. The problem I face is that I cannot find probe IDs in Ensemble mapping.

Could anyone help me with this? Probably biomaRt is a logical approach, but I cannot find it. I’m using alternative cdf from Brainarray.

 

I tried via xy coordinates (see below), but there is quite some redundancy and it is not comprehensive…

 

To make it more specific, below chunks of code that I’m currently using.

 

Thanks in advance!

Willem

 

 

# create probe intensity matrix for each probeset

for (i in 1:length(gNames)) {

      myProbeSet <- gNames[i]

      myPmindex <- unlist(pmindex(dataPreprocessed, myProbeSet))

      myDat <- intensity(dataPreprocessed)[myPmindex, ]

                  main = fProbeSet)

}

> head(myDat[,1:5])

        2720.CEL  2724.CEL  2725.CEL  2727.CEL  2728.CEL

442478 2335.2318  943.1485 2239.6485 2250.0652 2247.3568

975758 2695.0235 1232.8152 2923.0652 2794.6485 2889.9402

211794  924.3985  383.6485  856.5652  942.0652  803.8152

388714 1377.1485  764.0652 1404.8568 1622.5652 1447.1485

137675 4211.3152 2051.3985 4294.8985 4459.4818 3699.2318

985031 3602.1485 1634.2318 3607.2735 3501.6068 3442.6485

 

 

 

# load exon information

ensMap <- read.delim('../Mouse4302_Mm_ENSE_mapping.txt', sep = '\t')

> head(ensMap)

         Probe.Set.Name Chr Chr.Strand Chr.From Probe.X Probe.Y

1 ENSMUSE00000097912_at  10          -  6791726     451     421

2 ENSMUSE00000097912_at  10          -  6791765     724     625

3 ENSMUSE00000097912_at  10          -  6791790     613     565

4 ENSMUSE00000097912_at  10          -  6791850     147     367

5 ENSMUSE00000097912_at  10          -  6791866     790     251

6 ENSMUSE00000097912_at  10          -  6791883     405     115

  Affy.Probe.Set.Name

1          1451547_at

2          1451547_at

3          1451547_at

4          1451547_at

5          1451547_at

6          1451547_at

 

# link via xy coordinates

coord <- paste(ensMap$Probe.X, ensMap$Probe.Y, sep = '.')

 

> i2xy(as.numeric(rownames(myDat)))

        x   y

[1,] 595 441

[2,] 811 973

[3,] 371 211

[4,] 939 387

Willem Talloen

Janssen Pharmaceutica

Biostatistics and Programming GDO CoE

Turnhoutseweg 30, box 270

2340 Beerse 1

Belgium

Phone <a href="tel:%2B32%280%2914603434" value="+3214603434" target="_blank">+32(0)14603434       Fax <a href="tel:%2B32%280%2914605802" value="+3214605802" target="_blank">+32(0)14605802

[hidden email]

 

Janssen_Hor_RGB

 


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Users mailing list
[hidden email]
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Re: [BioMart Users] link probes to exons

Steffen Durinck-2
Hi Willem,

It looks like you have Ensembl exon IDs if you remove the "_at" from ENSMUSE00000097912_at.
You could use those Ensembl exon IDs to retrieve gene information from Ensembl through biomaRt.

Let me know if you need more help,
Steffen

On Thu, Nov 10, 2011 at 3:08 PM, Arek Kasprzyk <[hidden email]> wrote:
Hi Willen,
you need a biomaRt specialist Steffen here (cc'ed on this email)

a

On Thu, Nov 10, 2011 at 6:45 AM, Talloen, Willem [JRDBE] <[hidden email]> wrote:

Hi all,

 

I would like to link probes to exons as defined in Ensemble. The problem I face is that I cannot find probe IDs in Ensemble mapping.

Could anyone help me with this? Probably biomaRt is a logical approach, but I cannot find it. I’m using alternative cdf from Brainarray.

 

I tried via xy coordinates (see below), but there is quite some redundancy and it is not comprehensive…

 

To make it more specific, below chunks of code that I’m currently using.

 

Thanks in advance!

Willem

 

 

# create probe intensity matrix for each probeset

for (i in 1:length(gNames)) {

      myProbeSet <- gNames[i]

      myPmindex <- unlist(pmindex(dataPreprocessed, myProbeSet))

      myDat <- intensity(dataPreprocessed)[myPmindex, ]

                  main = fProbeSet)

}

> head(myDat[,1:5])

        2720.CEL  2724.CEL  2725.CEL  2727.CEL  2728.CEL

442478 2335.2318  943.1485 2239.6485 2250.0652 2247.3568

975758 2695.0235 1232.8152 2923.0652 2794.6485 2889.9402

211794  924.3985  383.6485  856.5652  942.0652  803.8152

388714 1377.1485  764.0652 1404.8568 1622.5652 1447.1485

137675 4211.3152 2051.3985 4294.8985 4459.4818 3699.2318

985031 3602.1485 1634.2318 3607.2735 3501.6068 3442.6485

 

 

 

# load exon information

ensMap <- read.delim('../Mouse4302_Mm_ENSE_mapping.txt', sep = '\t')

> head(ensMap)

         Probe.Set.Name Chr Chr.Strand Chr.From Probe.X Probe.Y

1 ENSMUSE00000097912_at  10          -  6791726     451     421

2 ENSMUSE00000097912_at  10          -  6791765     724     625

3 ENSMUSE00000097912_at  10          -  6791790     613     565

4 ENSMUSE00000097912_at  10          -  6791850     147     367

5 ENSMUSE00000097912_at  10          -  6791866     790     251

6 ENSMUSE00000097912_at  10          -  6791883     405     115

  Affy.Probe.Set.Name

1          1451547_at

2          1451547_at

3          1451547_at

4          1451547_at

5          1451547_at

6          1451547_at

 

# link via xy coordinates

coord <- paste(ensMap$Probe.X, ensMap$Probe.Y, sep = '.')

 

> i2xy(as.numeric(rownames(myDat)))

        x   y

[1,] 595 441

[2,] 811 973

[3,] 371 211

[4,] 939 387

Willem Talloen

Janssen Pharmaceutica

Biostatistics and Programming GDO CoE

Turnhoutseweg 30, box 270

2340 Beerse 1

Belgium

Phone <a href="tel:%2B32%280%2914603434" value="+3214603434" target="_blank">+32(0)14603434       Fax <a href="tel:%2B32%280%2914605802" value="+3214605802" target="_blank">+32(0)14605802

[hidden email]

 

Janssen_Hor_RGB

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users




_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users