User: tanyabioinfo

gravatar for tanyabioinfo
tanyabioinfo20
Reputation:
20
Status:
New User
Location:
Last seen:
2 weeks, 3 days ago
Joined:
11 months, 3 weeks ago
Email:
t***********@gmail.com

Posts by tanyabioinfo

<prev • 23 results • page 1 of 3 • next >
0
votes
0
answers
61
views
0
answers
(Closed) pheatmap RNA seq data
... Hi    I am plotting a pheatmap using following line in a R code pheatmap(counts_filtered_df,scale="row",cluster_col=FALSE,cluster_row=TRUE,border_color=NA,show_rownames = T)   I want to extract the row names in the same order as shown in pheatmap and the z scores for them.    So basically a n ...
rnaseq R pheatmap written 20 days ago by tanyabioinfo20
1
vote
1
answer
246
views
1
answer
RNAseq tximport Deseq2
...   HI I am using the tximport module to process the output of Salmon. Then I am using the vst(dds) to normalise the data. I understand that the assay for dds is count. How can I process the abundance(TPM) using the vst so that my TPM data is normalised.  My R code looks: txi <- tximport(files, ...
deseq2 tximport written 9 months ago by tanyabioinfo20 • updated 9 months ago by Michael Love19k
0
votes
1
answers
205
views
1
answers
Comment: A: RNA seq tximport
... Hi Michael   Thanks a lot. My TPM data is showing a lot of variation in terms of trends than RPM. Like the tximport output gives a lot of  variation among the replicates. Can you please help me why this would be happening.   Thanks   Tanya ...
written 10 months ago by tanyabioinfo20
0
votes
1
answer
205
views
1
answer
RNA seq tximport
... Hi I am using Salmon to process my RNA seq data. I just want to confirm that the abundance given as an output by the tximport package corresponds to TPM. Many of the cells (the output of tximport) have a value of zero which is making me think about this. Regards Tanya ...
tximport written 10 months ago by tanyabioinfo20
2
votes
2
answers
286
views
2
answers
tximport gene name
... Hi I am doing the following to get the tximport count  matrix with gene name in the first column txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame") txdf$symbol <- mapIds(EnsDb.Mmusculus.v79, txdf$gene_id, "GENENAME", "GENEID") tx2gene <- as.data.frame(txdf[,c("tx_id","sym ...
tximport written 10 months ago by tanyabioinfo20 • updated 10 months ago by Ed Siefker220
0
votes
1
answers
357
views
1
answers
Comment: A: PCA from TPM
... Hi Michael I am now using the follwoing code: txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE) sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time)) rownames(sampleTable) <- colnames(txi$counts) dds <- DESeqDataSe ...
written 10 months ago by tanyabioinfo20
1
vote
1
answer
357
views
1
answer
PCA from TPM
... Hi I am trying to do PCA analysis of my samples. I generated the matrix using the tximport package. I have transcript ids as my rows and the sample names are the columns. txi <- tximport(files, type="salmon", tx2gene=NULL, ignoreTxVersion=TRUE,dropInfReps=TRUE,txOut = TRUE) tpm <- (txi$abun ...
pca tpm tximport written 10 months ago by tanyabioinfo20
0
votes
3
answers
184
views
3
answers
Answer: A: RNA seq tximport
... Thanks James It worked for me.   ...
written 10 months ago by tanyabioinfo20
0
votes
3
answers
184
views
3
answers
RNA seq tximport
... Hi   I am using the following commands to run tximport txi <- tximport(files, type="salmon", tx2gene=tx2gene,ignoreTxVersion=TRUE,dropInfReps=TRUE) my tx2gene dataframe looks like this              tx_id            gene_id 1 ENSMUST00000082387 ENSMUSG00000064336 2 ENSMUST00000179436 ENSMUSG0 ...
tximport written 11 months ago by tanyabioinfo20
0
votes
1
answers
327
views
1
answers
Comment: C: PCA plot for TPM data
... Thanks Andy. Can you please help me how can I add colors to this PCA plot based on sample names.   Thanks   Tanya ...
written 11 months ago by tanyabioinfo20

Latest awards to tanyabioinfo

Popular Question 6 weeks ago, created a question with more than 1,000 views. For RNA Seq data analysis using Salmon and tximport

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 198 users visited in the last hour