Error while adding gene names

Question

[Kumar]

Hi, I am getting following ERROR. Please correct me in my script.

res$symbol <- mapIds(org.Hs.eg.db, 
                 keys=row.names(res), 
                 column="SYMBOL", 
                 keytype="ENSEMBL",
                 multiVals="first")

ERROR:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

[GenoMax]

Provide example of actual input going into this.

[Kumar]

Here is the input file.

$head(countdata$counts)
              sample1 sample2 sample3 sample4 sample5 sample6
 ENST00000631435.1       0       0       0       0       0       0
 ENST00000415118.1       0       0       0       0       0       0
 ENST00000434970.2       0       0       0       0       0       0
 ENST00000448914.1       0       0       0       0       0       0
 ENST00000632684.1       0       0       0       0       0       0
 ENST00000632524.1       0       0       0       0       0       0

[Kumar]

Here are some initial commands that I using before that process:

dds <- DESeq(dds)
res <- results(dds)
mcols(res, use.names=TRUE)
summary(res)
head(res)

I am using library("AnnotationDbi"), library("org.Hs.eg.db").

[Kumar]

these are ENSEMBL IDs. I am converting these into gene id.

[swbarnes2]

ENSEMBL ID is not helpful at all. Do you think you have protein IDs? Gene IDs?

[Kumar]

I have no gene IDs. I got these from the output of kallisto pipeline. I am not sure how to convert these ENSEMBL ID to gene ID. Please suggest how I can get gene IDs.

[GenoMax]

These are transcript ID's based on the list posted above.

[Kumar]

Yes! do I need to get gene IDs from these transcript IDs first before converting these to genes name?

[swbarnes2]

You have to understand what you have. Do you understand why your new code works and the old code didn't?

[swbarnes2]

Step1: are you absolutely sure that what you have is really gene names?

[Kumar]

I improved the script as following and it works. However, most of ENSEMBL IDs could not find Gene names.

res$symbol <- mapIds(org.Hs.eg.db, 
                 rownames(res)<-gsub("\\..*","",rownames(res)), 
                 column="SYMBOL", 
                 keytype = "ENSEMBLTRANS",
                 multiVals="first")

[swbarnes2]

Can you explain what you think that gsub line of code is doing?

[Kumar]

gsub is a function that perform replacement of the first and all matches respectively.

[swbarnes2]

You can't do bioinformatics like this; mindlessly quoting code you do not understand. It is a waste of time for people to help you when you do not understand your own work, and clearly have no interest in expending any energy to do so.

[Kumar]

Really! It is ridiculous. You did not give even a single line to solve my question and testing my knowledge. It is really pathetic. I don't know what is your problem for your frustration but this is the great community and people providing consistently support. No matter you are beginner or advance user. If you do not have time just do not reply. I do not know how you are proficient in coding you must be publishing one research paper every month (LOL). By the way, this is not my code I am just following DESeq2 tutorial. I know bioinformatics whatever I am required...

I do not know what do you think about research but I am surprised to know about your thought!

[jared.andrews07]

Think we all need to take a moment to cool our heads here - it can be frustrating for both sides. Manoj, it can be frustrating for regular members of the site to see questions that lack critical info. Try to take care to provide reproducible, clear, and complete examples of the issue you're facing prior to posting a question. Often, this process will help you figure out the answer yourself, but if not, it'll make it much easier for the community to help you more quickly. And @swbarnes2 somewhat has a point about using code you don't fully understand if you're just following a tutorial and can't determine why it's not working with your data.

Regardless, consider this a reminder to keep things civil.

[Ram]

The question was - "what is that line of code doing?", not "what does the function gsub do?".

You're modifying an object using the assignment operator while passing it as a parameter to a function. Are you sure that the assignment operation will yield the same type as rownames(res) would have?

If you wish to edit the rownames, do that before the function call.

Answer 1

[Arup Ghosh]

Use keytype = "ENSEMBLTRANS".