Question: Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
0
gravatar for Guiyuan Lei
11.9 years ago by
Guiyuan Lei90
Guiyuan Lei90 wrote:
Dear all, I am analyzing microarray data for Affymetrix yeast2 chip, I know that there are two organisms pombe and cerevisiae on this chip. I need to filter out pombe probesets. There are total 10928 probesets on yeast2 chip. How can I know which probeset is corresponding to pombe and which probeset is corresponding to cerevisiae? (1) I could get a list of probeset ID and genename from library "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. Are these 6356 probesets Cerevisiae probesets? (2) After I updated Bioconductor today, I found that the "yeast2GENENAME" contains total 10928 probesets! In latest version of Bioconductor, all probesets on yeast2 chip are included in "yeast2GENENAME", but there is no information about which probeset is pombe and which one is cerevisiae. Is there any new library/function which I can use to separate these 10928 probesets into cerevisie probesets and pombe ones? Many thanks! Best regards, Guiyuan
microarray yeast2 • 634 views
ADD COMMENTlink modified 11.9 years ago by Caroline Lemerle20 • written 11.9 years ago by Guiyuan Lei90
Answer: Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
0
gravatar for James W. MacDonald
11.9 years ago by
United States
James W. MacDonald51k wrote:
Hi Guiyuan, Download the Affy mask file: http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cerevisi ae.zip Then you can read in the s_cerevisiae.msk file using read.table() and subset your data accordingly. Best, Jim Guiyuan Lei wrote: > Dear all, > > I am analyzing microarray data for Affymetrix yeast2 chip, I know that > there are two organisms pombe and cerevisiae on this chip. I need to > filter out pombe probesets. There are total 10928 probesets on yeast2 > chip. How can I know which probeset is corresponding to pombe and > which probeset is corresponding to cerevisiae? > > (1) I could get a list of probeset ID and genename from library > "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. > Are these 6356 probesets Cerevisiae probesets? > (2) After I updated Bioconductor today, I found that the > "yeast2GENENAME" contains total 10928 probesets! In latest version of > Bioconductor, all probesets on yeast2 chip are included in > "yeast2GENENAME", but there is no information about which probeset is > pombe and which one is cerevisiae. Is there any new library/function > which I can use to separate these 10928 probesets into cerevisie > probesets and pombe ones? > > Many thanks! > > Best regards, > Guiyuan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENTlink written 11.9 years ago by James W. MacDonald51k
Answer: Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
0
gravatar for Caroline Lemerle
11.9 years ago by
Caroline Lemerle20 wrote:
Hi Guiyuan, I don't see it either but exactly that information is available for download on the manufacturer's website, here: http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cerevisi ae.zip http://www.affymetrix.com/Auth/support/downloads/mask_files/s_pombe.zi p file x contains the list of probesets from organism x on the yeast2 chip. On Nov 27, 2007 7:16 PM, Guiyuan Lei <guiyuanlei at="" gmail.com=""> wrote: > Dear all, > > I am analyzing microarray data for Affymetrix yeast2 chip, I know that > there are two organisms pombe and cerevisiae on this chip. I need to > filter out pombe probesets. There are total 10928 probesets on yeast2 > chip. How can I know which probeset is corresponding to pombe and > which probeset is corresponding to cerevisiae? > > (1) I could get a list of probeset ID and genename from library > "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. > Are these 6356 probesets Cerevisiae probesets? > (2) After I updated Bioconductor today, I found that the > "yeast2GENENAME" contains total 10928 probesets! In latest version of > Bioconductor, all probesets on yeast2 chip are included in > "yeast2GENENAME", but there is no information about which probeset is > pombe and which one is cerevisiae. Is there any new library/function > which I can use to separate these 10928 probesets into cerevisie > probesets and pombe ones? > > Many thanks! > > Best regards, > Guiyuan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 11.9 years ago by Caroline Lemerle20
Thank Jim and Caroline, I found that there are 5749 probesets in s_pombe.msk and 5028 probesets in s_cerevisiae.msk while there are total 10928 probesets on yeast2 chip. Does it mean that there are overlap between pombe and cerevisiae probesets? By the way, is there any smart way to use s_cerevisiae.msk to hide pombe probesets in cdf environment, i.e. use s_cerevisiae.msk as argument of some function so that R can only read cerevisiae probesets when do analysis? Best regards, Guiyuan On Nov 27, 2007 9:05 PM, Caroline Lemerle <caroline.lemerle at="" gmail.com=""> wrote: > Hi Guiyuan, > > I don't see it either but exactly that information is available for > download on the manufacturer's website, here: > > http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cerevi siae.zip > http://www.affymetrix.com/Auth/support/downloads/mask_files/s_pombe. zip > > file x contains the list of probesets from organism x on the yeast2 chip. > > > > On Nov 27, 2007 7:16 PM, Guiyuan Lei <guiyuanlei at="" gmail.com=""> wrote: > > Dear all, > > > > I am analyzing microarray data for Affymetrix yeast2 chip, I know that > > there are two organisms pombe and cerevisiae on this chip. I need to > > filter out pombe probesets. There are total 10928 probesets on yeast2 > > chip. How can I know which probeset is corresponding to pombe and > > which probeset is corresponding to cerevisiae? > > > > (1) I could get a list of probeset ID and genename from library > > "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. > > Are these 6356 probesets Cerevisiae probesets? > > (2) After I updated Bioconductor today, I found that the > > "yeast2GENENAME" contains total 10928 probesets! In latest version of > > Bioconductor, all probesets on yeast2 chip are included in > > "yeast2GENENAME", but there is no information about which probeset is > > pombe and which one is cerevisiae. Is there any new library/function > > which I can use to separate these 10928 probesets into cerevisie > > probesets and pombe ones? > > > > Many thanks! > > > > Best regards, > > Guiyuan > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >
ADD REPLYlink written 11.9 years ago by Guiyuan Lei90
Hi Guiyuan, Guiyuan Lei wrote: > Thank Jim and Caroline, > > I found that there are 5749 probesets in s_pombe.msk and 5028 > probesets in s_cerevisiae.msk while there are total 10928 probesets on > yeast2 chip. Does it mean that there are overlap between pombe and > cerevisiae probesets? Probably. The 151 unmasked probesets are too many to simply be the control probesets, but the only way to know for sure is to read Affy's documentation, and if that doesn't help, then contact Affy. > > By the way, is there any smart way to use s_cerevisiae.msk to hide > pombe probesets in cdf environment, i.e. use s_cerevisiae.msk as > argument of some function so that R can only read cerevisiae probesets > when do analysis? Take a look at the altcdfenvs package. Best, Jim > > Best regards, > Guiyuan > > On Nov 27, 2007 9:05 PM, Caroline Lemerle <caroline.lemerle at="" gmail.com=""> wrote: >> Hi Guiyuan, >> >> I don't see it either but exactly that information is available for >> download on the manufacturer's website, here: >> >> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cerev isiae.zip >> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_pombe .zip >> >> file x contains the list of probesets from organism x on the yeast2 chip. >> >> >> >> On Nov 27, 2007 7:16 PM, Guiyuan Lei <guiyuanlei at="" gmail.com=""> wrote: >>> Dear all, >>> >>> I am analyzing microarray data for Affymetrix yeast2 chip, I know that >>> there are two organisms pombe and cerevisiae on this chip. I need to >>> filter out pombe probesets. There are total 10928 probesets on yeast2 >>> chip. How can I know which probeset is corresponding to pombe and >>> which probeset is corresponding to cerevisiae? >>> >>> (1) I could get a list of probeset ID and genename from library >>> "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. >>> Are these 6356 probesets Cerevisiae probesets? >>> (2) After I updated Bioconductor today, I found that the >>> "yeast2GENENAME" contains total 10928 probesets! In latest version of >>> Bioconductor, all probesets on yeast2 chip are included in >>> "yeast2GENENAME", but there is no information about which probeset is >>> pombe and which one is cerevisiae. Is there any new library/function >>> which I can use to separate these 10928 probesets into cerevisie >>> probesets and pombe ones? >>> >>> Many thanks! >>> >>> Best regards, >>> Guiyuan >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 11.9 years ago by James W. MacDonald51k
Hi Jim, Many thanks. I have checked the s_pombe.msk and s_cerevisiae.msk files, the overlap between pombe and cerevisiae are probesets which with prefix "AFFX" and "RPTR". One strange thing is that one probeset called "177968_at" is in s_pombe.msk but is NOT among the whole 10928 probesets! So the overlap are 152 probesets. I got one more question, for the Yeast2GENENAME, many probesets only have ID, but no genename (is "NA"), is it possible to get gene name/symbol for all 10928 probesets? Best regards, Guiyuan On Nov 28, 2007 2:05 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Guiyuan, > > Guiyuan Lei wrote: > > Thank Jim and Caroline, > > > > I found that there are 5749 probesets in s_pombe.msk and 5028 > > probesets in s_cerevisiae.msk while there are total 10928 probesets on > > yeast2 chip. Does it mean that there are overlap between pombe and > > cerevisiae probesets? > > Probably. The 151 unmasked probesets are too many to simply be the > control probesets, but the only way to know for sure is to read Affy's > documentation, and if that doesn't help, then contact Affy. > > > > > By the way, is there any smart way to use s_cerevisiae.msk to hide > > pombe probesets in cdf environment, i.e. use s_cerevisiae.msk as > > argument of some function so that R can only read cerevisiae probesets > > when do analysis? > > Take a look at the altcdfenvs package. > > Best, > > Jim > > > > > > > Best regards, > > Guiyuan > > > > On Nov 27, 2007 9:05 PM, Caroline Lemerle <caroline.lemerle at="" gmail.com=""> wrote: > >> Hi Guiyuan, > >> > >> I don't see it either but exactly that information is available for > >> download on the manufacturer's website, here: > >> > >> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cer evisiae.zip > >> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_pom be.zip > >> > >> file x contains the list of probesets from organism x on the yeast2 chip. > >> > >> > >> > >> On Nov 27, 2007 7:16 PM, Guiyuan Lei <guiyuanlei at="" gmail.com=""> wrote: > >>> Dear all, > >>> > >>> I am analyzing microarray data for Affymetrix yeast2 chip, I know that > >>> there are two organisms pombe and cerevisiae on this chip. I need to > >>> filter out pombe probesets. There are total 10928 probesets on yeast2 > >>> chip. How can I know which probeset is corresponding to pombe and > >>> which probeset is corresponding to cerevisiae? > >>> > >>> (1) I could get a list of probeset ID and genename from library > >>> "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. > >>> Are these 6356 probesets Cerevisiae probesets? > >>> (2) After I updated Bioconductor today, I found that the > >>> "yeast2GENENAME" contains total 10928 probesets! In latest version of > >>> Bioconductor, all probesets on yeast2 chip are included in > >>> "yeast2GENENAME", but there is no information about which probeset is > >>> pombe and which one is cerevisiae. Is there any new library/function > >>> which I can use to separate these 10928 probesets into cerevisie > >>> probesets and pombe ones? > >>> > >>> Many thanks! > >>> > >>> Best regards, > >>> Guiyuan > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >
ADD REPLYlink written 11.9 years ago by Guiyuan Lei90
Hi Guiyuan, Guiyuan Lei wrote: > Hi Jim, > > Many thanks. I have checked the s_pombe.msk and s_cerevisiae.msk > files, the overlap between pombe and cerevisiae are probesets which > with prefix "AFFX" and "RPTR". One strange thing is that one probeset > called "177968_at" is in s_pombe.msk but is NOT among the whole 10928 > probesets! So the overlap are 152 probesets. > > I got one more question, for the Yeast2GENENAME, many probesets only > have ID, but no genename (is "NA"), is it possible to get gene > name/symbol for all 10928 probesets? You might check either netaffx or biomaRt, but if there are no gene names for certain probesets in the annotation package that usually indicates that the probesets in question interrogate things that have yet to be named (e.g., ESTs, inferred genes, etc). > > > Best regards, > Guiyuan > > On Nov 28, 2007 2:05 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: >> Hi Guiyuan, >> >> Guiyuan Lei wrote: >>> Thank Jim and Caroline, >>> >>> I found that there are 5749 probesets in s_pombe.msk and 5028 >>> probesets in s_cerevisiae.msk while there are total 10928 probesets on >>> yeast2 chip. Does it mean that there are overlap between pombe and >>> cerevisiae probesets? >> Probably. The 151 unmasked probesets are too many to simply be the >> control probesets, but the only way to know for sure is to read Affy's >> documentation, and if that doesn't help, then contact Affy. >> >>> By the way, is there any smart way to use s_cerevisiae.msk to hide >>> pombe probesets in cdf environment, i.e. use s_cerevisiae.msk as >>> argument of some function so that R can only read cerevisiae probesets >>> when do analysis? >> Take a look at the altcdfenvs package. >> >> Best, >> >> Jim >> >> >> >>> Best regards, >>> Guiyuan >>> >>> On Nov 27, 2007 9:05 PM, Caroline Lemerle <caroline.lemerle at="" gmail.com=""> wrote: >>>> Hi Guiyuan, >>>> >>>> I don't see it either but exactly that information is available for >>>> download on the manufacturer's website, here: >>>> >>>> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_cer evisiae.zip >>>> http://www.affymetrix.com/Auth/support/downloads/mask_files/s_pom be.zip >>>> >>>> file x contains the list of probesets from organism x on the yeast2 chip. >>>> >>>> >>>> >>>> On Nov 27, 2007 7:16 PM, Guiyuan Lei <guiyuanlei at="" gmail.com=""> wrote: >>>>> Dear all, >>>>> >>>>> I am analyzing microarray data for Affymetrix yeast2 chip, I know that >>>>> there are two organisms pombe and cerevisiae on this chip. I need to >>>>> filter out pombe probesets. There are total 10928 probesets on yeast2 >>>>> chip. How can I know which probeset is corresponding to pombe and >>>>> which probeset is corresponding to cerevisiae? >>>>> >>>>> (1) I could get a list of probeset ID and genename from library >>>>> "yeast2" (R command: as.list(yeast2GENENAME)), that is 6356 probesets. >>>>> Are these 6356 probesets Cerevisiae probesets? >>>>> (2) After I updated Bioconductor today, I found that the >>>>> "yeast2GENENAME" contains total 10928 probesets! In latest version of >>>>> Bioconductor, all probesets on yeast2 chip are included in >>>>> "yeast2GENENAME", but there is no information about which probeset is >>>>> pombe and which one is cerevisiae. Is there any new library/function >>>>> which I can use to separate these 10928 probesets into cerevisie >>>>> probesets and pombe ones? >>>>> >>>>> Many thanks! >>>>> >>>>> Best regards, >>>>> Guiyuan >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 11.9 years ago by James W. MacDonald51k
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