In the vignette "Description of Affy" it is sometimes shown tht the pm() and mm() functions will return the affyIDs as row names while the sample names as column names. When I execute this, though, using R 1.9.1 and affy 1.4.1 (I think), I just get a matrix with the sample names as column headers but no row.names. Also, in the vignette, it states you can get the affyids using probeNames. This works but the probeNames are not numbered as they are when returned (as it is shown then can be) using pm() or mm() (see page 14 of the vignette). So my question is two fold (sorry for the long winded explanation). How do I get mm() and pm() to return affyIDs with numbers OR can I take it for granted that the probeNames returned using probeNames are in order? I need to map the affyID to a specific sequence (ie compare sequence to Raw Intensity) and they differ based on the number. Thanks, Mark Larsen

It would probably be a good idea to obtain a newer version of R (2.1.0) and the Bioconductor affy package, and all its dependencies. At the top of page 13/14 (v1.5.8-1 / v1.6.7) in the affy vignette, the following code, > pm(affybatch.example, gn[100]) 20A 20B 10A D78156_at1 223.3 148.0 203.0 D78156_at2 149.8 155.5 131.0 D78156_at3 147.3 133.8 145.0 D78156_at4 162.3 131.8 134.0 D78156_at5 459.3 451.0 345.0 D78156_at6 711.0 526.8 601.8 D78156_at7 158.8 142.8 109.0 D78156_at8 219.0 211.3 167.0 D78156_at9 196.0 251.0 182.3 D78156_at10 1715.0 1291.8 1341.3 D78156_at11 710.5 506.3 553.0 D78156_at12 438.0 346.0 282.8 D78156_at13 439.0 311.3 387.0 D78156_at14 114.8 78.0 101.5 D78156_at15 114.0 87.0 89.5 D78156_at16 181.0 122.0 160.0 should give you the output you require, i.e. specifying a vector of affy ids as arguements to pm and mm adds row.names for the individual probes. Marcus p.s. packageDescription("affy", field="Version") gives you your version of the affy package, 'version' describes your R install. >>> Mark Larsen <larsenmtl@comcast.net> 1/06/2005 4:40:51 a.m. >>> In the vignette "Description of Affy" it is sometimes shown tht the pm() and mm() functions will return the affyIDs as row names while the sample names as column names. When I execute this, though, using R 1.9.1 and affy 1.4.1 (I think), I just get a matrix with the sample names as column headers but no row.names. Also, in the vignette, it states you can get the affyids using probeNames. This works but the probeNames are not numbered as they are when returned (as it is shown then can be) using pm() or mm() (see page 14 of the vignette). So my question is two fold (sorry for the long winded explanation). How do I get mm() and pm() to return affyIDs with numbers OR can I take it for granted that the probeNames returned using probeNames are in order? I need to map the affyID to a specific sequence (ie compare sequence to Raw Intensity) and they differ based on the number. Thanks, Mark Larsen _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}

Marcus, Thanks, I'm smacking myself in the forehead on that one.... I'll be working on upgrading soon. In a corporate environment all software has to be re-validated with the new versions. It makes for a headache. Thanks again, Mark > > It would probably be a good idea to obtain a newer version of R (2.1.0) and the > Bioconductor affy package, and all its dependencies. > > At the top of page 13/14 (v1.5.8-1 / v1.6.7) in the affy vignette, the following > code, > > > pm(affybatch.example, gn[100]) > 20A 20B 10A > D78156_at1 223.3 148.0 203.0 > D78156_at2 149.8 155.5 131.0 > D78156_at3 147.3 133.8 145.0 > D78156_at4 162.3 131.8 134.0 > D78156_at5 459.3 451.0 345.0 > D78156_at6 711.0 526.8 601.8 > D78156_at7 158.8 142.8 109.0 > D78156_at8 219.0 211.3 167.0 > D78156_at9 196.0 251.0 182.3 > D78156_at10 1715.0 1291.8 1341.3 > D78156_at11 710.5 506.3 553.0 > D78156_at12 438.0 346.0 282.8 > D78156_at13 439.0 311.3 387.0 > D78156_at14 114.8 78.0 101.5 > D78156_at15 114.0 87.0 89.5 > D78156_at16 181.0 122.0 160.0 > > should give you the output you require, i.e. specifying a vector of affy ids as > arguements to pm and mm adds row.names for the individual probes. > > Marcus > > p.s. packageDescription("affy", field="Version") gives you your version of the > affy package, 'version' describes your R install. > > > >>> Mark Larsen <larsenmtl@comcast.net> 1/06/2005 4:40:51 a.m. >>> > In the vignette "Description of Affy" it is sometimes shown tht the pm() > and mm() functions will return the affyIDs as row names while the sample > names as column names. When I execute this, though, using R 1.9.1 and > affy 1.4.1 (I think), I just get a matrix with the sample names as > column headers but no row.names. Also, in the vignette, it states you > can get the affyids using probeNames. This works but the probeNames are > not numbered as they are when returned (as it is shown then can be) > using pm() or mm() (see page 14 of the vignette). > > So my question is two fold (sorry for the long winded explanation). How > do I get mm() and pm() to return affyIDs with numbers OR can I take it > for granted that the probeNames returned using probeNames are in order? > I need to map the affyID to a specific sequence (ie compare sequence > to Raw Intensity) and they differ based on the number. > > Thanks, > > Mark Larsen > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > ______________________________________________________ > > The contents of this e-mail are privileged and/or confidential to the > named recipient and are not to be used by any other person and/or > organisation. If you have received this e-mail in error, please notify > the sender and delete all material pertaining to this e-mail. > ______________________________________________________