how to perform cross platform gene expression analysis

Hi all,

I am trying to find differential expressed genes(DEG) among different platforms(cross platform).

I know that at first the shared genes among different platforms must be detected. But I don't know how to do that.

Can anybody give me a clue how to perform the above task?

Thank u in advance

Nazanin

differentially-expressed-genes r cross-platform

• 2,029 views • link

updated 4.2 years ago by Ram

• written 11.4 years ago by nazaninhoseinkhan

1 answer

Generally people would use Combat from the SVA package to try and correct for the inter-platform batch effect and then use the corrected values for the DE analysis.

• 0 views • link

written 11.4 years ago by Devon Ryan

More posts like this

how to generate CNVplot from variant effect predictor result
written 7.8 years ago by nazaninhoseinkhan

Dear all, I got the results of VEP for copy number alteration and now I want to generate CNVplot. Can you advise me how to …
removing outliers before running DESeq2
written 8.0 years ago by nazaninhoseinkhan

Dear all, After running DESeq2 program successfully I found out that I had to detect and remove outliers from my htseq count datasets before running …
Heatmap: edgeR counts and DEG
written 8.1 years ago by RiNG •

I have used edgeR in Galaxy to perform differential expression analysis. As output I have 3 files with a list of differentially expressed genes (comparison …
Illumina BeadChip Array probe file Vs control probe file
written 8.3 years ago by nazaninhoseinkhan

Hi every body, I want to get the list of differential expressed genes from an Illumina BeadChip Array data set (Gse22155). In Limma manual it …
Removing batch effects between Affymetrix and Agilent platforms using ComBat
written 8.3 years ago by nazaninhoseinkhan

Dear all, I want to integrate microarray data from different platforms (Affymetrix and Agilent). I know that ComBat function which is now is a part …
The proper order of defining groups in GEO2R
written 8.6 years ago by nazaninhoseinkhan

Dear all, I used GEO2R to find the list of differential expressed genes between cancer and normal tissue. I did not know the expression of …
Is it correct to consider the genes of grey module resulted from consensus network analysis (WGCNA)…
written 8.6 years ago by nazaninhoseinkhan

Dear all, I have pre and post treatment microarray samples. I performed differential expression analysis to find list of differential expressed genes. In parallel I …
Choosing appropriate FPKM cutoff for finding differential expressed genes
written 9.8 years ago by nazaninhoseinkhan

Hi every body, I want to analyze the results of Cuffdiff. Cuffdiff has detected 149 significant differential expressed genes. However, some genes have FPKM=0 (no …
How to find targets for large number of lncRNAs
written 9.9 years ago by nazaninhoseinkhan

Dear all, I have 1500 lncRNA (both IDs and Sequences) and I wish to find their targets. Can anybody suggest me any database to do …
Downloading data from TCGA
written 10.2 years ago by nazaninhoseinkhan

Dear all, I have a question about searching data from the cancer genome atlas (TCGA). I want to know if it has any data about …