BIO RAD CFX MANAGER THRESHOLD HOW TO
BIO RAD CFX MANAGER THRESHOLD SOFTWARE

In addition, we found that the magnitude of the upregulation is highly subtype-specific, being the HER2+ cells the model with lowest HOXB7 upregulation, presenting very low or even null expression for HOXB8 and HOXB9, respectively. We showed that HOXB7 is upregulated in all breast cancer cells analyzed, while HOXB8 and HOXB9 are significantly upregulated in MCF7 (Luminal A), BT474 (Luminal B) and MDA231 cells (Triple-negative Claudin-low). This technique allows a very sensitive quantification of gene expression and was performed using the fluorophore SYBR Green in order to obtain the expression levels relative to a reference gene, GAPDH in this case. Here, we provided the analyses of HOXB7, HOXB8 and HOXB9 expression profiles in cell lines extensively used in the literature addressing the putative role of HOXB genes in breast cancer (MCF7, BT474, SKBR3, MDA231 and MDA468) and representative of the clinical breast cancer molecular subtypes (Luminal A, Luminal B, HER2+ and Triple-negatives Claudin-low/Basal), compared to a normal breast model (MCF10A), using quantitative-PCR (qPCR). However, due to breast cancer complexity and heterogeneity, added to the use of different technical approaches, the observed expression profiles are sometimes contradictory. I was wondering about the possiblity of using limma in these datasets.Alterations in HOXB genes expression in breast cancer have been described and related to therapy response and disease progression. Maybe I shall log transform the percentage data if can be used for limma analysis? highly lableing % certainly is favored as for good compounds. Another dataset we have is compound labeling high throghput assays for interested protein at intended sites/pockets as percentage levels of successful labeling, data ranged from 0 to 100%. What about other types of high-thoughput data that can be used for limma analysis? Is there a way or general principle/rule to assess whether the data types/distribution etc is suitable for limma analysis to derive differential features between interested contrasting groups? for example, one dataset I wish to use limma was derived from high-throughput assays, and had been scaled between around -2 and 1 (and we can essentially treat the data as log2 intensity like in microrray and high values mean highly expressed etc for the same probe after normalized), since more posiitve and more negative have opposite biological meanings. I want to follow up this topic for limma: I have used limma method for many occasions of microarray datasets in the past, but besides microarrays, RNA-seq (with voom) and quantitative PCR data as mentioned here. Ultimately I'd like to transform the Ct values in expression values that I can fit into an ExpressionSet object and feed to lmFit() and downstream functions.

BIO RAD CFX MANAGER THRESHOLD SOFTWARE

The built-in gene expression analysis module in CFX Manager software lets you immediately turn your results into answers, without data export. So, here's my question: how should I process the qPCR Ct data for use in limma? 102 101 100 10-1 10-2 Target Normalized fold expression IL1-b Tubulin 0 Hr 1 Hr 2 Hr Decrease in IL1-bxpressione and increase in tubulin expression over experiment time-course. в€†в€†Ct = в€†Ct (treated sample) вЂ“ в€†Ct (untreated sample)Д«ut this only works for very simple experimental designs/contrasts (e.g.: treated vs untreated), while I have a more complex study design that would benefit from the statistical modelling capabilities of limma. Then one can calculate the difference across conditions of interest as в€†в€†Ct values: в€†Ct = Ct (gene of interest) вЂ“ Ct (housekeeping gene) These Ct values are then typically normalized by subtracting the Ct values of reference/housekeeping genes to derive в€†Ct values:

BIO RAD CFX MANAGER THRESHOLD HOW TO

However, that's the only time qPCR gets mentioned, and I haven't found examples on how to work with this type of data.ДЇor background, qPCR data comes in the form of cycle threshold (Ct) values, which are inversely correlated to the gene expression (the more the gene is expressed, the fewer cycles it will need to reach the threshold). Microarrays, RNA-seq and quantitative PCR. To data from any quantitative gene expression technology including The linear model and differential expression functions are applicable

Bio rad cfx manager threshold