Hey,
I'm working on a project and I just started with bioinformatics, so I don't know much in this field. I'm looking at the GEO dataset on NCBI. The dataset gives me normalized signal intensity values and i wanted to know which genes are differentially expressed and was wondering if there is a way to calculate that from the values provided?
Thanks in advance.
If you have signal intensity values from two different conditions. For differential expression, you have to do a statistical test(T-test and ANOVA) which tells you the significant differences between two conditions. The type of test based on the structure of data, for this you need knowledge on the statistics.
The data in one columnrefers to a measurement of a sample (this sample can be an indivdual, a pool of individuals or some "biological" sample).
The data one row referes to one particular gene.
The data is a (normalized) signal that should be proportional to the (relative) abundance of the particular target sequence in a particular sample. If the experiment was a dual-color hybridization, the data could also be the signal intensity ratio.
Actually, the data should be the log(signal) or log(signal ratio). This should be described in the file.
If the data are log(signal), you can calculate the log(signal ratio) as a simple mean difference of the data in the respective columns. If the data are log(signal ratios), then the data represents already the result for the compared samples. Finding other comparisons is a bit complicated but can be done, for instance, with limma [https://bioconductor.org/packages/release/bioc/html/limma.html].
Thanks for your response. My data has two samples and the scanned images were analyzed using feature extraction software (Agilent). It is log2 transformed, quantile normalized and base line transformed using the median of the samples. The data contains agilent color microarray information and the corresponding values. I'm trying to understand if I can get gene annotations for this and get the expression values. I don't understand what the values correspond to.
ID_REF VALUE
GE_BrightCorner -0.23861122
DarkCorner -0.09232402
A_23_P117082 0.60445786
A_33_P3246448 -0.8994918
A_33_P3318220 -0.06654954
A_33_P3236322 -0.2543733
A_33_P3319925 0.24735403
A_21_P0000509 -2.0573397
I'm trying to understand what these values mean and if they relate to gene expression values?
Thanks in advance.
Your data is Processed/normalized,two-colour experiment data used to draw the conclusions from your study. Two-color experiments (e.g., Cy3/Cy5) will typically have log (test/control) ratios; one-color experiments will have normalized signal intensity.In the two-color cDNA platform, mRNA from two samples is reverse-transcribed to cDNA, labeled with fluorescent dye, Cy3 (green) or Cy5 (red), and simultaneously hybridized to an array containing spots of DNA sequences. Ratios of fluorescence intensities provide a relative measure of gene expression at each spot on the array. For more information about your data refer this link
http://www.ncbi.nlm.nih.gov/geo/info/geo_agil.html
There should be a GEO platform mentioned (GPL-number). There you find what the values in the columns "ID_REF" refer to. Another option to get the annotations is through BioMart, and finally you can possibly downlowad the annotations from Agilent directly (Agilent eArray) - but I don't know if this needs any log-in.
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