Hello all, pardon me for asking a simple question. in an affy experiment where one sample per one chip is used, it is very clear for me that an affy cel file is derived from one sample. So in the raw data I have, an affy study has 20 normal samples, 40 prostate cancer and final 40 neoplastic prostate tissues. So a total of 100 affy cel files (from 100 chips, 100 samples) are made. In a cDNA experiment, from the raw data, it is very difficult for me to identify which samples is used for cy3 and which sample is used for cy5. How can I have intensity for a cy3 tagged sample and cy5 tagged sample. For example in the link given below: http://llmpp.nih.gov/lymphoma/data/rawdata/ Lymphoma chip is used. It is my understanding that all cDNAs know to be part of lymphoma are printed on this chip. Here the first sample is mentioned as lc8n076 as Blood B cells. When I click the data link I see Ch1 mean Ch2 mean, ch1 median and ch2 median values. In this case how do I know why sample is reference sample tagged with cy3 and which sample is tagged with cy5. I am asking a simple question, and sincerly I do not know to the answer and I am seeking help of scientists who have a lot of experience to help me in understnding this concept. I really appreaciate your help. Thank you. Srini Iyyer

Hi At the top of one of the data files I opened is: REMARK CH1 IMAGE lc8n076_532 nm REMARK CH2 IMAGE lc8n076_635 nm Now the numbers 532 and 635 stand out (because I know about these things) - 532 is the scanning frequency of Cy3, and 635 the scanning frequency of 635. So for this data set, Ch1 is Cy3 and Ch2 Cy5. It may change for each data set though! (and this is why data shoule be released in a MIAME compliant format....) :-) Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Srinivas Iyyer Sent: Thu 12/23/2004 5:49 AM To: bioconductor@stat.math.ethz.ch Cc: Subject: [BioC] cDNA raw data Hello all, pardon me for asking a simple question. in an affy experiment where one sample per one chip is used, it is very clear for me that an affy cel file is derived from one sample. So in the raw data I have, an affy study has 20 normal samples, 40 prostate cancer and final 40 neoplastic prostate tissues. So a total of 100 affy cel files (from 100 chips, 100 samples) are made. In a cDNA experiment, from the raw data, it is very difficult for me to identify which samples is used for cy3 and which sample is used for cy5. How can I have intensity for a cy3 tagged sample and cy5 tagged sample. For example in the link given below: http://llmpp.nih.gov/lymphoma/data/rawdata/ Lymphoma chip is used. It is my understanding that all cDNAs know to be part of lymphoma are printed on this chip. Here the first sample is mentioned as lc8n076 as Blood B cells. When I click the data link I see Ch1 mean Ch2 mean, ch1 median and ch2 median values. In this case how do I know why sample is reference sample tagged with cy3 and which sample is tagged with cy5. I am asking a simple question, and sincerly I do not know to the answer and I am seeking help of scientists who have a lot of experience to help me in understnding this concept. I really appreaciate your help. Thank you. Srini Iyyer _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

In short, one has to be "told" by the experimenter. There is not a standard (nor should there be) for hybridization. However, for storing and reporting data, there IS a standard which is followed less often than it should be. Sean On Dec 23, 2004, at 12:49 AM, Srinivas Iyyer wrote: > Hello all, > pardon me for asking a simple question. in an affy > experiment where one sample per one chip is used, it > is very clear for me that an affy cel file is derived > from one sample. So in the raw data I have, an affy > study has 20 normal samples, 40 prostate cancer and > final 40 neoplastic prostate tissues. So a total of > 100 affy cel files (from 100 chips, 100 samples) are > made. > > In a cDNA experiment, from the raw data, it is very > difficult for me to identify which samples is used for > cy3 and which sample is used for cy5. How can I have > intensity for a cy3 tagged sample and cy5 tagged > sample. > > For example in the link given below: > http://llmpp.nih.gov/lymphoma/data/rawdata/ > > Lymphoma chip is used. It is my understanding that all > cDNAs know to be part of lymphoma are printed on this > chip. Here the first sample is mentioned as lc8n076 > as Blood B cells. When I click the data link I see > Ch1 mean Ch2 mean, ch1 median and ch2 median values. > In this case how do I know why sample is reference > sample tagged with cy3 and which sample is tagged with > cy5. > > I am asking a simple question, and sincerly I do not > know to the answer and I am seeking help of scientists > who have a lot of experience to help me in > understnding this concept. I really appreaciate your > help. > > Thank you. > > Srini Iyyer > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor