Gene Expression Analysis using R?

More Leonid Ouchanov's questions See All

Buffered Growth Medium for Bacteria?

If I buffer a liquid growth medium with PBS (say I use 100 mL of PBS and 900 mL of dd H20 to dissolve the required amount of dried liquid medium) and my starting pH is 7, how effective would it be...

04 May 2019 10,168 2 View

Suggestions on H2O2 Detection (colorimetry)?

Hello, I am trying to design a simple assay whereby I could measure various concentrations of peroxide in an analyte. Copper sulphate gives nice color gradation upon addition of peroxide and...

02 March 2019 783 2 View

Real Time PCR Analysis and Normalization?

If I measure gene expression in an organism under two different conditions, do I still need to normalize these genes to a housekeeping gene or comparison between the genes under two different...

11 December 2018 3,636 3 View

Hippurate Hydrolysis Microplate ?

Hi, I'd like to adapt hippurate hydrolysis test to microplate reader. Has anyone done this before, maybe? I assume both Na hippurate and ninhydrin must be available as powder? The question is...

06 July 2018 3,252 0 View

Buffer system for Bacterial co-Incubation?

So, I need to grow two bacteria in one medium without letting the pH go below 5.5 and without any negative effect on bacterial growth. Which buffer would be more suitable? I read on Sigma that...

06 July 2018 4,642 0 View

Published Primers not Working?

So, I have some primer pairs from a publication that work in silico, but do not give me any PCR product. I tried all annealing temperatures, upped Mg++, did trouchdown PCR-no result. Anyone has...

02 March 2018 1,074 12 View

How do you get Rid of Nonspecific Bands in PCR?

So, here is what I am dealing with: The Tm of the primers is 55 for the forward one and 56 for the reverse one. In -silico PCR produces 750 BP band, but in reality I get 3 bands. The third one...

02 March 2018 4,732 16 View

IDT's Oligo Analizer 3.1?

Anyone used this before? I suspect one of the oligos of my primer pair forms a hairpin ? I just don't know how to read the output oligo analyzer gives. This primer is from a publication and they...

02 March 2018 8,558 1 View

Can anyone explain the FAFLP Principle?

Hi, It seems that this method has advantages over PFGE when it comes to distinguishing bacterial strains, however the principle of this method remains elusive. What I do not understand is the...

31 December 2017 1,913 3 View

Is that C. jejuni?

Can someone take a look and confirm whether what I isolated is indeed C. jejuni? I haven't got any primers yet, so I can't confirm by PCR, but the culture is gram negative, catalaze +, oxidase +....

02 March 2017 4,546 13 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

09 August 2024 7,718 0 View

How are iso-frequency contours plotted?

Let's say we have a standard, regular hexagonal honeycomb with a 3-arm primitive unit cell (something like the figure attached; the figure is only representative and not drawn to scale). The...

07 August 2024 1,937 1 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

How to normalize and take the significance of the MTT OD values with 3 replicates for the same cell-line?

Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...

07 August 2024 8,106 4 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

Ajit kumar Roy

Download freely available software from net.

Jochen Wilhelm

limma and DEseq

Ayman Amin

Some Packages (to install from Bioconductor):

DESeq2
clusterProfiler
DOSE
org.Hs.eg.db
pathview
DEGreport

Leonid Ouchanov

Thank you ! :)

Yes, Dan Powell , very new to R and still figuring it out, thank you for your response.

Greeshma Thulasi

Hi,

Do you have microarray expression data?

You can use Bioconductor, https://www.bioconductor.org/install/ which is a bioinformatic suit with lot of in-built packages within it.

install by: source("https://bioconductor.org/biocLite.R")

packages can be found here : https://www.bioconductor.org/packages/release/bioc/

You can search different packages, based on your data and read the description and usage by reading the vignette

Thanks, Greeshma Thulasi No data yet, but it is going to be qPCR data. I am preparing in advance.