User: Nithisha

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Nithisha10
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4 months ago
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Posts by Nithisha

<prev • 40 results • page 1 of 4 • next >
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Reading in delta Ct values using HTqPCR
... Hi everyone, I have one csv file that contains the delta Ct values for several samples (columns) and genes as row names. I have samples from different Groups, Grp A, Grp B and Grp C. My data columns look something like this. Samples in Group A and B start with baseline disease condition while Group ...
htqpcr written 19 days ago by Nithisha10 • updated 17 days ago by Gordon Smyth32k
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Comment: C: Performing differential gene analysis on RT PCR experimental data
... Thank you Davis. ...
written 19 days ago by Nithisha10
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Comment: C: Best way to design a contrast matrix for analysis of dataset
... Hi Aaron, I am so sorry about this oversight, I did not realize. Thanks for your patience! ...
written 23 days ago by Nithisha10
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Performing differential gene analysis on RT PCR experimental data
... Hi everyone,  I had a question with regards to a GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92776. The link says that this data contains expression profiling from RT PCR and so if I downloaded the raw non-normalized data at the bottom of the page, would the values there be g ...
differential gene expression written 23 days ago by Nithisha10 • updated 17 days ago by Gordon Smyth32k
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Comment: C: Best way to design a contrast matrix for analysis of dataset
... Hi Aaron, I am not sure why the error pops up.  I first entered the command:  groups <- factor(paste0(es$profile,'.',es$group_id))' which gives me:  > groups [1] BASELINE.B BASELINE.B BASELINE.B BASELINE.B BASELINE.B BASELINE.B BASELINE.B BASELINE.B [9] BASELINE.B BASELINE.B ...
written 23 days ago by Nithisha10
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Answer: A: Best way to design a contrast matrix for analysis of dataset
... Hi Aaron, Thank you so much for pointing this out to me, it is very helpful indeed! However, when I go back to the Limma manual, it says "Since we need to make comparisons both within and between subjects, it is necessary to treat Patient as a random effect" on page 49 and I was wondering if you co ...
written 26 days ago by Nithisha10
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Best way to design a contrast matrix for analysis of dataset
... Hi all, I have this data set https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92776, in which there are 337 blood samples from patients. This is from a Lupus study and so Group A consists of 41 patients who were waned off their Standard of Care (SoC) medications till a flare (aggravation of SL ...
limma written 4 weeks ago by Nithisha10
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Comment: C: Standardizing gene symbols
... Thank you! I shall try this out as well. ...
written 12 weeks ago by Nithisha10
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Comment: C: Standardizing gene symbols
... Thanks a lot Gordon.  I do have a few questions though. For your code, I did not completely understand what  fit$genes$Official.Symbol refers to. Is that pointing to a dataframe within another dataframe? I used this: dfl$Official_Symbol <- alias2SymbolTable(df$gene, species="Mm") where df i ...
written 12 weeks ago by Nithisha10
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Solve overlapping gene labels in volcano plot when using textxy
... Hi everyone,  This is the code I used to create a volcano plot: I am trying to plot several genes and highlight the top 20 most downregulated and top 20 most downregulated genes using green and red. #Plot a volcano plot library(calibrate) head(afinal) threshold.high <- afinal$logFC[20] ...
R written 3 months ago by Nithisha10

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