I m a first year student so this question might seem a little dense. but currently I ran PCR analysis of some gene. I got the potential interesting genes from the microarray data from the geo data. first time i run the PCR, the Ct value was high. when i ask my supervisor, he ask me to check the raw expression level that if the raw expression value is low, it could be a possible problem. but there is only comparative expression level(log2FC). could it be that i couldn't find or is there a case that the researcher didn't upload the raw expression level on the geo data?
hi Htoo Shwe Eain yes in some cases as we have seen the researcher would not submit raw data but the QC data should help you ascertain what measures were done to the data. Sometimes raw data and QCed data are uploaded but Geo does not have any restrictions and variations exist in type of data uploaded.
Hello Rabea Al-Temaimi,
it is not very likely, that GEO has accepted only derived data of the chips. Try to find CEL files (raw data) or CHP files (with GCOS software generated data) if you have found Affymetrix chips. CEL files could be analyzed using for example RMAExpress and then you have a possibility to find the expression values of your gene. If you want you could send me the GEO accession number and then I will check it.
Hi Htoo
first you need to admit is that both technologies are not same and difference in results are common, bias are different.
there can be lot of solutions, what I suggest is first to make your own analysis on the raw data, see where probes map compared to your primers (more all have been designed at 5' and best it is), and look for the primers (make an silico PCR in UCSC or NCBI primerBlast) and if you got the possibility check for the quality of the design (I use always Oligo7 to design (licensed soft)).
all the best
fred
- Badges
- Science method