Normalized Error Bars
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group with error bars on the relative expression histograms in a qPCR study. I have a question regarding to the representation of the relative expression histograms. We did a comparative qPCR study, and, using the Pfaffl's efficiency corrected Ct formula, I calculated the relative expression values for all standard error of normalized data of my samples. Since I have biological replicates, I get error bars for the treatment groups
Qpcr Fold Change Error Bars
on the relative expression values, but in many papers I noticed that they also use error bars for the control groups (value 1 with an z score procedure error bar). How? Topics PCR × 5,013 Questions 71,925 Followers Follow Real-Time PCR × 2,151 Questions 3,370 Followers Follow Feb 12, 2013 Share Facebook Twitter LinkedIn Google+ 2 / 0 All Answers (3) Jo Vandesompele · Ghent University Biogazelle's qbasePLUS software delta delta ct calculation (http://www.qbaseplus.com) can do this. If you want to do this manually in a spreadsheet, I would need a bit more information on how EXACTLY you did you calculations. If you calculated relative quantities for all you samples at once (e.g. according to Hellemans et al., Genome Biology, 2007), you will also have variable results for your control group and hence an error bar for this group. Feb 13, 2013 Jack M Gallup · Iowa State University Dr. V, your software is the best
Error Propagation
in the world for this. It's good to let the cat out of the bag at this point. And it is always good to hear your opinion on qPCR stats. The error bars for the controls is always propotional to their error bars before the control was divided by itself. I believe this is also equal to the coefficient of variance. E.g., if the error bar for a control value of 0.5 was +/- 0.2 (before control was divided by itself), then, when the control becomes "1" by self-division, the error bar becomes (by proportion or coefficient of variance rules) +/- 0.4. But if the error bars are the result of transformation from log to linear scale, the error bar above and below the median is not symmetrical... technically, and thus a more lengthy explanation is needed. Error just doesn't simply disappear... must always be accounted for - and very tricky, unless you use Dr. V's and Dr. H's software. Feb 14, 2013 Jochen Wilhelm · Justus-Liebig-Universität Gießen I do not see the point of showing the "normalized controls" as a bar of height 1 - with or without error bars. This value (rel. conc = 1) should better be represented a a horizontal line. Actually, it is the x-xasis to what the other values refer to. This is what thie normalization does. Form the "treated" group(s), you get a delta-ct for each sample, similarily for the "control" group. Then you average the delta-cts for each group
MetaFilter querying the hive mind Log In Sign Up MetaFilter AskMeFi FanFare Projects Music Jobs IRL MetaTalk More Best Of Podcast Chat Labs Search MetaFilter… Menu Home FAQ About Archives Tags Popular Random Why leave out that one error bar? January 24, 2006 3:37 PM Subscribe A statistics / scientific convention question. I've noticed in scientific journals that often when a set of data is presented with values normalized how to normalize data to one of the sample groups, and the value for that sample group is arbitrarily set to 1, 10, 100 or whatever, to simplify interpretation, the variability/error data for that one sample group is left out. Is there a good statistical reason for that or is it just some random convention with no good reason? Here's an example: you have a set of data on the height of trees according to their https://www.researchgate.net/post/How_to_represent_control_group_with_error_bars_on_the_relative_expression_histograms_in_a_qPCR_study age (say trees that are 5, 10 and 20 years old). You calculate the mean height and standard deviation for each age group. For whatever reason, you want to normalize the mean values for all three groups to the 5-year-old group and set that value to 1 to present the data. My question is why would people not show the standard deviation (adjusted for the normalization) for the 5-year-old group along http://ask.metafilter.com/31427/Why-leave-out-that-one-error-bar with those for the other two groups. posted by shoos to Science & Nature (17 answers total) I had a long explanation, but I couldn't explain it very well anyway, so here's a shorter one: To account for different outside conditions when an experiment is repeated at a different time, it's often useful to always normalize to an internal control that was taken the same day as the original data set. So on April 11 you measure something and normalize to the April 11 control, and on May 15 you repeat the experiment and normalize to the May 15 control. That way you rule out external influences that are very different on both days. (Maybe the airco was on in May but not yet in April.) Since they're both normalized to the internal control, both sets of data have a 100% control sample, and other variations are really due to whatever you're measuring. I can't explain this very well at all, and it doesn't fit with the tree example. But basically: the sets were individually set to the normalized value, and the error given is the one AFTER normalization (so it's 0 for the one that it's normalized to)posted by easternblot at 3:59 PM on January 24, 2006 Easternblot, I understand w
Overview Keeping a lab notebook Writing research papers Dimensions & units Using figures (graphs) Examples of graphs Experimental error Representing error Applying statistics Overview Principles of microscopy http://www.ruf.rice.edu/~bioslabs/tools/data_analysis/errors_curvefits.html Solutions & dilutions Protein assays Spectrophotometry Fractionation & centrifugation Radioisotopes and detection Error Representation and Curvefitting As far as the laws of mathematics refer to reality, they are https://plot.ly/~xiangpeng/69/normalized-fluorescent-intensity-vs-rinsing-number.embed not certain; and as far as they are certain, they do not refer to reality --- Albert Einstein (1879 - 1955) This article is a follow-up to error bars the article titled "Error analysis and significant figures," which introduces important terms and concepts. The present article covers the rationale behind the reporting of random (experimental) error, how to represent random error in text, tables, and in figures, and considerations for fitting curves to experimental data. You might also be interested in our tutorial normalized error bars on using figures (Graphs). When to report random error Random error, known also as experimental error, contributes uncertainty to any experiment or observation that involves measurements. One must take such error into account when making critical decisions. When you present data that are based on uncertain quantities, people who see your results should have the opportunity to take random error into account when deciding whether or not to agree with your conclusions. Without an estimate of error, the implication is that the data are perfect. Random error plays such an important role in decision making, it is necessary to represent such error appropriately in text, tables, and in figures. When we study well defined relationships such as those of Newtonian mechanics, we may not require replicate sampling. We simply select enough intervals at which to collect data so that we are confident in the relationship. Connecting the data points is then sufficient, although it may be desirable to use error bars t
intensity in the y-axis.. The x-axis shows values from -0.308800536073 to 5.30880053607. The y-axis shows values from -0.0695159135216 to 1.07082246852.