Affymetrix genechip miRNA array analysis
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@jordi-altirriba-gutierrez-682
Last seen 3.5 years ago
Dear Biocoductor users, I would like to analyse the presence of some microRNA in a tissue under different conditions. I am thinking on using the Affymetrix GeneChip miRNA array (launched on March 2009), as our institution has an Affymetrix platform (suggestions from other platforms are welcomed). I was wondering how to proceed after the hybridization. In other words, can I proceed as a gene expression array (mRNA)? (rma -> limma, for example) Or are there other specific methods in order to normalize the data, to observe its quality and to get differential expression? The miRNA arrays are different from gene expression arrays as there are 4 identical probes for each miRNA and 11 probes for sno/scaRNA. Moreover, there aren’t mismatch probes. Many thanks for your help and suggestions. Jordi Altirriba Hospital Clinic Barcelona, Spain _________________________________________________________________ [[alternative HTML version deleted]]
miRNA limma microRNA miRNA limma microRNA • 2.3k views
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@jordi-altirriba-gutierrez-682
Last seen 3.5 years ago
Sorry for the previous mail in not plain text. Here is in plain text: Dear Biocoductor users, I would like to analyse the presence of some microRNA in a tissue under different conditions. I am thinking on using the Affymetrix GeneChip miRNA array (launched on March 2009), as our institution has an Affymetrix platform (suggestions from other platforms are welcomed). I was wondering how to proceed after the hybridization. In other words, can I proceed as a gene expression array (mRNA)? (rma -> limma, for example) Or are there other specific methods in order to normalize the data, to observe its quality and to get differential expression? The miRNA arrays are different from gene expression arrays as there are 4 identical probes for each miRNA and 11 probes for sno/scaRNA. Moreover, there aren?t mismatch probes. I have just read that Christian Stratowa proposed the use of rma (http ://article.gmane.org/gmane.science.biology.informatics.conductor/24682 /match=mirna), but at this moment I don?t have found that anybody has given positive or negative feedback to his mail. Many thanks for your help and suggestions. Jordi Altirriba Hospital Clinic Barcelona, Spain _________________________________________________________________ Chatea sin l?mites en Messenger con la tarifa plana de Orange
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Dear Jordi, Until now I did not receive any feedback to my mail. Please note that rma does only use PM probes, so the missing mismatch probes do not matter. Furthermore, the manual for the Affymetrix "miRNA QC Tool" mentions that you can set the tool to use rma, however, I could not test it, since the version that I have downloaded is missing the "Save" button for this purpose which is shown in the corresponding figure of the manual. You can download the tool from: http://www.affymetrix.com/partners_programs/programs/developer/tools/d evnettools.affx#1_1 Personally, I do not have any experience with miRNA and have only access to the three CEL-files which you can download from Affymetrix. Thus, I am afraid that I cannot give you any helpful suggestions. Best regards Christian Jordi Altirriba wrote: > Sorry for the previous mail in not plain text. > Here is in plain text: > > Dear Biocoductor users, > I would like to analyse the presence of some microRNA in a tissue under different conditions. > I am thinking on using the Affymetrix GeneChip miRNA array (launched on March 2009), as our institution has an Affymetrix platform (suggestions from other platforms are welcomed). > I was wondering how to proceed after the hybridization. In other words, can I proceed as a gene expression array (mRNA)? (rma -> limma, for example) Or are there other specific methods in order to normalize the data, to observe its quality and to get differential expression? > The miRNA arrays are different from gene expression arrays as there are 4 identical probes for each miRNA and 11 probes for sno/scaRNA. Moreover, there aren?t mismatch probes. > I have just read that Christian Stratowa proposed the use of rma (ht tp://article.gmane.org/gmane.science.biology.informatics.conductor/246 82/match=mirna), but at this moment I don?t have found that anybody has given positive or negative feedback to his mail. > > Many thanks for your help and suggestions. > > Jordi Altirriba > Hospital Clinic > Barcelona, Spain > _________________________________________________________________ > Chatea sin l?mites en Messenger con la tarifa plana de Orange > > _______________________________________________ > 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 > >
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Hi, you can download the CDF from Affymetrix, so you *should* be able to run a simple affy and limma analysis; however there are lots of different species on this chip, so you may want to subset probes to the relevant ones for your species prior to the limma analysis (my version of the affy miRNAQCtool keeps crashing, so I can't use it to normalise even the example files downloaded from Affy) cheers, Mark ----------------------------------------------------- Mark Cowley, PhD Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- On 08/10/2009, at 6:01 AM, cstrato wrote: > Dear Jordi, > > Until now I did not receive any feedback to my mail. > Please note that rma does only use PM probes, so the missing > mismatch probes do not matter. > Furthermore, the manual for the Affymetrix "miRNA QC Tool" mentions > that you can set the tool to use rma, however, I could not test it, > since the version that I have downloaded is missing the "Save" > button for this purpose which is shown in the corresponding figure > of the manual. You can download the tool from: > http://www.affymetrix.com/partners_programs/programs/developer/tools /devnettools.affx#1_1 > Personally, I do not have any experience with miRNA and have only > access to the three CEL-files which you can download from > Affymetrix. Thus, I am afraid that I cannot give you any helpful > suggestions. > > Best regards > Christian > > Jordi Altirriba wrote: >> Sorry for the previous mail in not plain text. >> Here is in plain text: >> >> Dear Biocoductor users, >> I would like to analyse the presence of some microRNA in a tissue >> under different conditions. >> I am thinking on using the Affymetrix GeneChip miRNA array >> (launched on March 2009), as our institution has an Affymetrix >> platform (suggestions from other platforms are welcomed). >> I was wondering how to proceed after the hybridization. In other >> words, can I proceed as a gene expression array (mRNA)? (rma -> >> limma, for example) Or are there other specific methods in order >> to normalize the data, to observe its quality and to get >> differential expression? The miRNA arrays are different from gene >> expression arrays as there are 4 identical probes for each miRNA >> and 11 probes for sno/scaRNA. Moreover, there aren?t mismatch probes. >> I have just read that Christian Stratowa proposed the use of rma (h ttp://article.gmane.org/gmane.science.biology.informatics.conductor/24 682/match=mirna >> ), but at this moment I don?t have found that anybody has given >> positive or negative feedback to his mail. >> >> Many thanks for your help and suggestions. >> Jordi Altirriba >> Hospital Clinic >> Barcelona, Spain >> _________________________________________________________________ >> Chatea sin l?mites en Messenger con la tarifa plana de Orange >> >> _______________________________________________ >> 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
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