Gene Expression Analysis using R?

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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 10,010 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 643 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 3,483 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 3,112 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 4,480 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 877 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 4,561 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 8,436 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 1,777 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 4,393 13 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 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.