Dear Dr. Friedman, Thank you for the notes again. It was really helpful and my many questions got cleared after going through it. But what my adviser asking me to do is, i've normalized data (54 k probes), he's asking me to functionally group them all. After that, he wants me to perform significance test within each group to find out deferentially expressed genes. My question is how's that different from conventional way of finding DE genes and functionally grouping them ?? Is it valid?? Dear Sean, I've data from HGU133 plus 2 array. I followed through the links but still i'm confused. I've attached a file for reference [this'a screen shot of a published data]. In the attachment, the transcript audacin 3 gamma, is represented by 4 different probe ID's and all are showing different intensity values. Now i want filter those probe ID's with significant deviation, from further analysis. How do i get this data of different probe's representing the same trascript ?? Again sorry if my questions are lame, i'm new to microarray analysis and i'm getting confused and lost. On Wed, Nov 30, 2011 at 8:16 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Wed, Nov 30, 2011 at 2:04 AM, anand mt [guest] > <guest at="" bioconductor.org=""> wrote: > > > > Hi all.. > > > > i have following questions. > > > > 1) How many probesets represent a gene on microarray chip ? > > > > That depends on the array platform. For a given platform, you can use > the annotation packages to answer this question. To get started, take > a look at: > > http://bioconductor.org/help/workflows/annotation-data/ > > > 2) How do i access raw intesity value of probes (before normalization) ? > > This will depend on the array platform and the software package you > are using to do your analysis. Some specifics are probably needed. > To get started, be sure to take a look at: > > http://bioconductor.org/help/workflows/oligo-arrays/ > > > 3) Do i need to read cdf file to do that ?? > > Generally not. Depending on the software package that applies, the > data from the CDF file are usually repackaged for use in bioconductor. > Again, some specifics of your data and experiment are important. > > > 4) After pre-processing the data and normalization, we generally go for > significance tests and gene grouping. My question is, if i group the genes > before performing significance test (say now i have 3 groups based on > apoptosis,cell cycle, DNA replication) and then perform significance test > within each group, will the results be same as that of conventional way ?? > Is it a valid method to do so?? > > > > You might take a look at this question and response on biostar: > > > http://biostar.stackexchange.com/questions/14796/gene-expression- analysis-microarrays-geneset > > Hope that helps. > > Sean > > > > Sorry if my questions are silly. > > > > -- output of sessionInfo(): > > > > --NONE-- > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- ****************************************************************** Anand M.T School of Biotechnology (Bio-Informatics), International Instituteof Information Technology (I2IT), P-14, Rajiv Gandhi Infotech park, Hinjewadi, Pune-411 057. INDIA. "The secret of success comprised in three words.. Work, Finish & Publish" - Michael Faraday

On Fri, Dec 2, 2011 at 12:35 AM, anand m t <anandrox05 at="" gmail.com=""> wrote: > Dear Dr. Friedman, > > Thank you for the notes again. It was really helpful and my many questions > got cleared after going through it. > But what my adviser asking me to do is, i've normalized data (54 k probes), > he's asking me to functionally group them all. > After that, he wants me to perform significance test within each group to > find out deferentially expressed genes. > My question is how's that different from conventional way of finding DE > genes and functionally grouping them ?? Is it valid?? If your advisor is asking you to do this, you should discuss all of the above with him not with people on this email list who have no background. Based on your interpretation of what your advisor asks you to do, I would say it is certainly different from what a "standard" analysis is. When discussing this with your advisor you might want to ask him whether he is aware that affymetrix arrays typically have many probes grouped into probesets. You might want to discuss how you could go about "functionally group them". Wrt. the last question you might want to look at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/g enomic_curated_CDF.asp and read the references on that page. Please don't ask us to interpret what your advisor is asking you to do. Kasper > > Dear Sean, > > I've data from HGU133 plus 2 array. I followed through the links but still > i'm confused. I've attached a file for reference [this'a screen shot of a > published data]. > In the attachment, the transcript audacin 3 gamma, is represented by 4 > different probe ID's and all are showing different intensity values. > Now i want filter those probe ID's with significant deviation, from further > analysis. How do i get this data of different probe's representing the same > trascript ?? > > Again sorry if my questions are lame, i'm new to microarray analysis and > i'm getting confused and lost. > > > On Wed, Nov 30, 2011 at 8:16 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Wed, Nov 30, 2011 at 2:04 AM, anand mt [guest] >> <guest at="" bioconductor.org=""> wrote: >> > >> > Hi all.. >> > >> > i have following questions. >> > >> > 1) How many probesets represent a gene on microarray chip ? >> > >> >> That depends on the array platform. ?For a given platform, you can use >> the annotation packages to answer this question. ?To get started, take >> a look at: >> >> http://bioconductor.org/help/workflows/annotation-data/ >> >> > 2) How do i access raw intesity value of probes (before normalization) ? >> >> This will depend on the array platform and the software package you >> are using to do your analysis. ?Some specifics are probably needed. >> To get started, be sure to take a look at: >> >> http://bioconductor.org/help/workflows/oligo-arrays/ >> >> > 3) Do i need to read cdf file to do that ?? >> >> Generally not. ?Depending on the software package that applies, the >> data from the CDF file are usually repackaged for use in bioconductor. >> ?Again, some specifics of your data and experiment are important. >> >> > 4) After pre-processing the data and normalization, we generally go for >> significance tests and gene grouping. My question is, if i group the genes >> before performing ?significance test (say now i have 3 groups based on >> apoptosis,cell cycle, DNA replication) and then perform significance test >> within each group, will the results be same as that of conventional way ?? >> Is it a valid method to do so?? >> > >> >> You might take a look at this question and response on biostar: >> >> >> http://biostar.stackexchange.com/questions/14796/gene-expression- analysis-microarrays-geneset >> >> Hope that helps. >> >> Sean >> >> >> > Sorry if my questions are silly. >> > >> > ?-- output of sessionInfo(): >> > >> > --NONE-- >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org. >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > > > > -- > ****************************************************************** > Anand M.T > School of Biotechnology (Bio-Informatics), > International Instituteof Information Technology (I2IT), > P-14, Rajiv Gandhi Infotech park, > Hinjewadi, > Pune-411 057. > INDIA. > > "The secret of success comprised in three words.. Work, Finish & Publish" - > Michael Faraday > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Anand, I am not sure what you advisor means by "functionally group". Best wishes, Rich On Fri, 2 Dec 2011, anand m t wrote: > Dear Dr. Friedman, > > Thank you for the notes again. It was really helpful and my many questions > got cleared after going through it. > But what my adviser asking me to do is, i've normalized data (54 k probes), > he's asking me to functionally group them all. > After that, he wants me to perform significance test within each group to > find out deferentially expressed genes. > My question is how's that different from conventional way of finding DE > genes and functionally grouping them ?? Is it valid?? > > Dear Sean, > > I've data from HGU133 plus 2 array. I followed through the links but still > i'm confused. I've attached a file for reference [this'a screen shot of a > published data]. > In the attachment, the transcript audacin 3 gamma, is represented by 4 > different probe ID's and all are showing different intensity values. > Now i want filter those probe ID's with significant deviation, from further > analysis. How do i get this data of different probe's representing the same > trascript ?? > > Again sorry if my questions are lame, i'm new to microarray analysis and > i'm getting confused and lost. > > > On Wed, Nov 30, 2011 at 8:16 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Wed, Nov 30, 2011 at 2:04 AM, anand mt [guest] >> <guest at="" bioconductor.org=""> wrote: >>> >>> Hi all.. >>> >>> i have following questions. >>> >>> 1) How many probesets represent a gene on microarray chip ? >>> >> >> That depends on the array platform. For a given platform, you can use >> the annotation packages to answer this question. To get started, take >> a look at: >> >> http://bioconductor.org/help/workflows/annotation-data/ >> >>> 2) How do i access raw intesity value of probes (before normalization) ? >> >> This will depend on the array platform and the software package you >> are using to do your analysis. Some specifics are probably needed. >> To get started, be sure to take a look at: >> >> http://bioconductor.org/help/workflows/oligo-arrays/ >> >>> 3) Do i need to read cdf file to do that ?? >> >> Generally not. Depending on the software package that applies, the >> data from the CDF file are usually repackaged for use in bioconductor. >> Again, some specifics of your data and experiment are important. >> >>> 4) After pre-processing the data and normalization, we generally go for >> significance tests and gene grouping. My question is, if i group the genes >> before performing significance test (say now i have 3 groups based on >> apoptosis,cell cycle, DNA replication) and then perform significance test >> within each group, will the results be same as that of conventional way ?? >> Is it a valid method to do so?? >>> >> >> You might take a look at this question and response on biostar: >> >> >> http://biostar.stackexchange.com/questions/14796/gene-expression- analysis-microarrays-geneset >> >> Hope that helps. >> >> Sean >> >> >>> Sorry if my questions are silly. >>> >>> -- output of sessionInfo(): >>> >>> --NONE-- >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > > > -- ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Biomedical Informatics Shared Resource Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "The last 250 pages of the last Harry Potter book took place in one day because alot happened in that day. All of Ulysses takes place in one day and nothing happened in that day." -Rose Friedman, age 11