gene expression of specifics gene

I want to compare the gene expression of Diabetes type 2 for my experiment.

I have 3 samples: control, after treatment (drug A), After treatment (drug B).

There are about 20 genes relevant to the Genetics of type 2 diabetes. Is there any instruction on how to use a heat map for these genes in R?

I appreciate if you share me the link.

my second question: do you have an instruction/pipeline for KEGG diabetes type 2 pathway map?

rna-seq

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written 5.0 years ago by Bioinformatics1 •

You did not mentions what kind of instruction do you need?

Do you need the instruction to make a heatmap of these 20 genes? Are you already using any package like pheatmap or something?
Yes there are pipelines. One of them is using Gage

https://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

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written 5.0 years ago by Hyper_Odin

Thanks for the link.

I imported the data into R

But, how draw a heat map for 20 genes?

I have lof2FC of each sample. How do I do the heatmap? Thanks in advance

 >mydata <- read.csv("C:/Users/.../Downloads/ diabetestype2.csv")
> df <- data.frame(mydata)
> print (df)

Gene     X1STD      X2Cin   X3Met  
1           GRK6  2.063400  0.0000000 -0.3733
.
.
.
> metaData <- read.csv('C:/Users/lazim/Downloads/metadata.csv ', header = TRUE, sep = ",")
> metaData 

    id dex    Drug Geoid
1 1STD   B Notreat GSM14
2 2Cin   A     Cin GSM15
3 3Met   C     Met GSM19

> mypalette <- brewer.pal(11,"RdYlBu")

> morecols <- colorRampPalette(mypalette)

> col.cell <- c("purple","orange")[ metaData$id]

> heatmap.2(df,col=rev(morecols(50)),trace="none", main="Top 72 most relevant genes across samples in type 2 diabetes",ColSideColors=col.cell,scale="row")

**Error in heatmap.2(df, col = rev(morecols(50)), trace = "none", main = "Top 72 most relevant genes across samples in type 2 diabetes",  :   could not find function "heatmap.2"**

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updated 5.0 years ago by Ram

• written 5.0 years ago by Bioinformatics1 •

You're doing lots of posts, all of them related to R errors. Did you read the manuals for EdgeR or DEseq2?? Every post is related to this subject. Did you load the gplot package? Please, read the manuals, show some effort in resolving those kinds of errors. A simple google search for this error will give you the answer!

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written 5.0 years ago by brunobsouzaa

You don't have necessary package installed/loaded in your workspace.

If already installed then do this- library("gplots")
If not then this- install.packages("gplots")

This might help https://biocorecrg.github.io/CRG_RIntroduction/heatmap-2-function-from-gplots-package.html

If you are using R for the first time, please ask for help from your colleagues or as @brunobsouzaa suggested go through the basics of using R

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written 5.0 years ago by Hyper_Odin

Thanks Hyper-Odin

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written 5.0 years ago by Bioinformatics1 •

I have log2(Fold Change) for two groups. Is there any instruction/pipelines I can use for gene expression using log2(Fold Change) in R?

My second question? less than <? is downregulated and more than >? upregulated? Do you have instructions for that using log2(Fold Change)?

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written 5.0 years ago by Bioinformatics1 •

Again, you did not mention the kind of pipeline you want for gene expression !
It is completely up to you what should be your cutoff value. You should refer to similar papers. Generally it varies between ±0485 to ±0.585 (log2fold change) which converts to 1.4 -1.5 in terms fold change

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written 5.0 years ago by Hyper_Odin

HelloHyper_Odin , NEBNext Ultra II + Full QC, Library Prep Kit (Illumina) and sequenced with NextSeq, HO150c single read).

I download log2fold change from basespaceIllumina in csv format.

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written 5.0 years ago by Bioinformatics1 •

Still lack of information or you don't know what you want to do... If you already have the log2fold change, it means that those files went through some pipeline and gave you those results. If you want to know how to build a heatmap, follow this topic. Another thing you can do is to use reactome to analyze your DE genes.

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written 5.0 years ago by brunobsouzaa

What does it mean Status: OK, or Low in RNA analysis?

Gene:WASH7P
Status:OK
log2(Fold Change): 0.05
q Value:1.00E+00
Significant: FALSE enter image description here

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written 5.0 years ago by Bioinformatics1 •

This comment above is completely out of context. Please edit the toplevel question and add a precise question. Otherwise this question might be deleted as it is basically a collection of comments without any content. As Hyper_Odin said already there is currently not enough details to add any answer.

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written 5.0 years ago by ATpoint

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